Affymetrix Molecular Diagnostic Software User s Guide IVD. For in vitro diagnostic use Rev. B

Transcription

1 Affymetrix Molecular Diagnostic Software User s Guide IVD For in vitro diagnostic use Rev. B 07/2008

2 Limited License Limited License. Subject to the Affymetrix terms and conditions that govern your use of Affymetrix products, Affymetrix grants you a non-exclusive, non-transferable, nonsublicensable license to use this Affymetrix product only in accordance with the manual and written instructions provided by Affymetrix. You understand and agree that except as expressly set forth in the Affymetrix terms and conditions, that no right or license to any patent or other intellectual property owned or licensable by Affymetrix is conveyed or implied by this Affymetrix product. In particular, no right or license is conveyed or implied to use this Affymetrix product in combination with a product not provided, licensed or specifically recommended by Affymetrix for such use. Trademarks Affymetrix, GeneChip,, HuSNP, GenFlex, Flying Objective, CustomExpress, CustomSeq, NetAffx, Tools To Take You As Far As Your Vision, The Way Ahead, Powered by Affymetrix, GeneChip-compatible, and Command Console are trademarks of Affymetrix, Inc. All other trademarks are the property of their respective owners. Patents Products may be covered by one or more of the following patents and/or sold under license from Oxford Gene Technology: Arrays products may be covered by one or more of the following patents: U.S. Patent Nos. 5,445,934; 5,744,305; 5,945,334; 6,140,044; 6,261,776; 6,291,183; 6,346,413; 6,399,365; 6,420,169; 6,551,817; 6,610,482; 6,733,977; 6,955,915 and D430,024 and other U.S. or foreign patents. Products are manufactured and sold under license from OGT under 5,700,637 and 6,054,270. Software products may be covered by one or more of the following patents: U.S. Patent Nos. 5,733,729; 5,795,716; 5,974,164; 6,066,454; 6,090,555; 6,185,561; 6,188,783; 6,223,127; 6,228,593; 6,229,911; 6,242,180; 6,308,170; 6,361,937; 6,420,108; 6,484,183; 6,505,125; 6510,391; 6,532,462; 6,546,340; 6,687,692; 6,607,887; 7,062,092 and other U.S. or foreign patents. Fluidics Stations may be covered by U.S. Patent Nos. 6,114,122; 6,287,850; 6,391,623; 6,422,249; and other U.S. or foreign patents. AutoLoaders may be covered by one or more of the following patents: U.S. Patent Nos. 6,511,277; 6,604,902; 6,705,754; 7,108,472; and other U.S. or foreign patents. Use of the GeneChip WT Amplified Double-Stranded cdna Synthesis and Amplification Kit in accordance with the instructions provided is accompanied by a limited license to U.S. Patent Nos. 5,716,785; 5,891,636; 6,291,170; and 5,545,522. Users who do not purchase this Kit may be required to obtain a license under these patents or to purchase another licensed kit. Copyright Affymetrix, Inc. All Rights Reserved.

3 i CONTENTS Chapter 1 Welcome to AMDS 7 Introduction 7 Intended Use 7 System Description 8 Terminology 11 How This Guide Is Organized 13 Conventions Used in This Guide 13 Resources 15 Other Documentation 15 Technical Support 16 Chapter 2 AMDS Overview 19 Introduction 19 Assay Workflow 20 Description of Assay Workflow Steps 21 Preparing The Target Sample 22 Creating, Editing and Deleting the Test Request 22 Registering the Test Request 22 Hybridizing the Test Request Assay 23 Washing and Staining the Array in the Fluidics Station 24 Scanning the Test Request Assay the AutoLoaderDx 25 Computing Cell Intensities 25 Displaying and Archiving Test Results 26 Chapter 3 AMDS User Interface and Workflow 27 Introduction 27 The AMDS Application 28

4 ii The AMDS User s Guide Rev. B The AMDS User Interface 28 Workflows and Worklists 29 The Left Panel The Workflow 29 The Center Panel The Worklists 31 Active Worklist 32 Registration Worklist 33 Hybridization Worklist 34 Fluidics Worklist 35 Scanner Worklist 36 Reviewing Test Results 37 Non-Active Worklist 38 The Right Panel User and Instrument Details 39 User Details 40 Device Status 40 Alerts 42 Alert Details and Recommended Resolution 42 Roles and Privileges 42 The Administrator Panel 43 Administrator Functions 44 Chapter 4 Test Request Processing 45 Introduction 45 AMDS Quick Reference Guide 45 Using the Barcode Reader 51 Handling the Array Cartridge 52 Starting AMDS 54 Turning on the System 54 Changing Your Password 57 Logging Off 58 Shutting Down 59 Managing Test Requests 60 Creating, Editing and Cancelling Test Requests The Active Worklist 60 Creating the Test Request 61

5 contents iii Editing Test Requests 65 Deleting Test Requests 67 Cancelling Test Requests 68 Associating Reagent Lot Numbers to Multiple Test Requests Assay Batch 70 Registering a Test Request 71 Processing Test Requests 75 Hybridizing an Array 76 Washing and Staining an Array in the Fluidics Station 81 Scanning an Array 85 Scanning the Array in Normal Operational Mode 86 Scanning Arrays in Manual Mode Manual Scan 87 Stopping a Scan 88 Adding Arrays During a Scanning Run 88 Reviewing Test Results 89 Batch Analysis Assay 92 Chapter 5 The AMDS Administrative Features 95 Quick Reference Guide 95 Viewing Logs 102 System Logs 102 Audit Logs 103 Managing the Assay 105 Installing an Assay 105 Installing a Certificate 106 Deactivating an Assay 107 Managing the Users 109 Adding a User 109 Editing a User 111 Managing the System 113 Changing the Instrument Settings 113 Managing the Fluidics Station 114 Managing the Workstation 116 Managing the Printer 117

6 iv The AMDS User s Guide Rev. B Managing the Firewall Settings 119 Viewing Instrument Service Logs 120 Archiving Test Requests 121 Setting the General Configuration 122 Chapter 6 AMDS Troubleshooting 127 Introduction 127 First Type of Problem Resolving Instrument Related Errors 128 Second Type of Problem Resolving Individual Test Requests Errors 129 Third Type of Problem Resolving Operational and Data Input Errors 129 Resolving Alerts 130 Resolving Alerts Procedure 131 Instrument Troubleshooting 132 Fluidics Station 133 AutoLoader 133 Appendix A The Fluidics Station 450Dx 135 Introduction 135 Warnings and Precautions 136 Instrument Components 138 Using the Fluidics Station 450Dx 141 Assay Documentation 141 Using the Barcode Reader with the Fluidics Station 142 The Fluidics Station 450Dx Protocols 142 Setting Up an Assay 143 Sample Hybridization Protocol Using the Fluidics Station 143 Sample Staining Protocol 144 Operating the Fluidics Station 145 Starting the Fluidics Station 145 Running a Fluidics Station Protocol 146 Shutting Down 156 Fluidics StationDx Care and Maintenance 160 Introduction 160

7 contents v Instrument Care 160 Fluidics Station Bleach Protocol 160 The Bleach Cycle 161 The Rinse Cycle 166 Peristaltic Tubing Maintenance 169 Setting the Peristaltic Tubing Maintenance Parameters 169 Replacing the Peristaltic Tubing Procedure 171 Fluidics Station Troubleshooting and Assistance 173 Troubleshooting Decision Tree 173 Problems and Solutions 176 Meaning of Error Messages 180 Other Problems and Solutions 182 FS450Dx LCD Messages 184 The FS450Dx Instrument Specifications 187 Regulatory Compliance 188 CE Mark Declaration of Conformity 188 Regulatory 189 China RoHS Restriction of Hazardous Substances Compliance 190 SJ/T 电子信息产品污染控制标识要求 192 Appendix B The Scanner 3000Dx with AutoLoaderDx 195 Introduction 195 Safe Operation 196 When to Contact Affymetrix 197 Laser Safety 197 Electrical Safety 199 Workstation - AutoLoader Connections 200 Connecting the Barcode Reader 203 AutoLoaderDx Indicator Lights and On/Off Button 204 Scanning Arrays 207 Using Tough-Spots to Prevent Leaks 207 Loading Arrays into the Carousel 208 Loading the Carousel into the AutoLoaderDx 210 Starting the AutoLoaderDx 212 Shutting Down the AutoLoaderDx 212

8 vi The AMDS User s Guide Rev. B Cleaning and Maintenance 213 Configuring the AutoLoaderDx 213 Troubleshooting 214 Troubleshooting the AutoLoaderDx 214 Issues Relating to the AutoLoaderDx s Operation 215 Troubleshooting the AutoLoaderDx 217 AutoLoaderDx Error Messages 218 Manually Removing a Lodged Array Cartridge 220 The AutoLoaderDx Specifications 224 Regulatory Compliance 225 CE Mark Declaration of Conformity 225 Regulatory 227 China RoHS Restriction of Hazardous Substances Compliance 228 SJ/T 电子信息产品污染控制标识要求 231 Index 235

9 Chapter1 WELCOME TO AMDS Introduction Welcome to the Affymetrix Molecular Diagnostic Software (AMDS) User's Guide. The AMDS User's Guide provides details concerning both the workflow and administrator functions of the AMDS part of the Affymetrix Microarray Instrumentation System. AMDS Quick Reference Card (p/n ) is a complement to this user guide and provides an overview of AMDS. This manual explains how to use the AMDS to: Create and process test requests and generate test results Perform administrative tasks such as: Managing user properties Performing systems management Installing, activating, and deactivating assays Viewing and archiving logs and records Intended Use The Affymetrix GeneChip Microarray Instrumentation System, consisting of the GeneChip 3000Dx v.2 scanner with AutoLoaderDx, FS450Dx v.2 fluidics station and the Affymetrix Molecular Diagnostics Software, is intended to measure fluorescence signals of labeled DNA target hybridized to GeneChip arrays. WARNING: Operators are responsible for following internal security policies to ensure security of patient data.

10 8 The AMDS User s Guide Rev. B System Description AMDS controls the assay work flow process of the Affymetrix Microarray Instrumentation System. The goal of the Microarray Instrumentation System is to produce a final test result based on the Affymetrix GeneChip array technology. At the end of assay process, the software provides this test result in the form of a report that you can print and which the software archives as a file for further analysis. AMDS is part of the larger Microarray Instrumentation System application suite. This suite consists three parts: 1. Affymetrix Software Developer s Kit (ASDK) this provides the assay developer with all the tools necessary for the creation of a specific assay sofware module for use on the AMDS system. 2. Assay Software Module this provides all the parameters necessary to process a specific Affymetrix GeneChip array from hybridization through fluidics to scanning to create a meaningful test result. AMDS identifies a particular assay software module by the Assay Name. 3. AMDS this guides the user through all the steps necessary to process a GeneChip array as a Test Request that uses the Assay Name as the blueprint to control the various array processes from hybridization though fluidics, scanning, log keeping and result printing and archiving. NOTE: This user s guide deals only with the AMDS application. AMDS is part of the Affymetrix GeneChip array laboratory system and works in connection with the following hardware (Figure 1.1 and Figure 1.2). A workstation equipped with a hardware firewall and installed with AMDS The Affymetrix GeneChip Fluidics Station 450Dx v.2 (aka the fluidics station)

11 chapter 1 Welcome to AMDS 9 - For more detailed information about the fluidics station, see the appendix, The Fluidics Station 450Dx, on page 135 The Affymetrix GCS3000 Scanner with AutoLoaderDx - For more detailed information about the scanner- AutoLoaderDx, see the appendix, The Scanner 3000Dx with AutoLoaderDx, on page 195. A printer A barcode reader An uninterruptible power supply IMPORTANT: Depending on the particular assay, the system may also require a hybridization, or incubation, oven to aid in hybridizing the specimen to the array. This item is not part of the Microarray Instrumentation System. Figure 1.1 Schematic of the Microarray Instrumentation System hardware

12 10 The AMDS User s Guide Rev. B Figure 1.2 The Microarray Instrumentation System major hardware components: Fluidics Station 450Dx, workstation terminal and GCS3000 Scanner with AutoLoaderDx You can also use a barcode reader to enter barcode information such as that found on the following items: the GeneChip array cartridge, the fluidics station, the specimen identification, the reagent lot number and other identification information. (Figure 1.3). See the section, Using the Barcode Reader, on page 51 for more information on using the barcode reader. Figure 1.3 The barcode reader

13 chapter 1 Welcome to AMDS 11 You may use your own hybridization oven. Affymetrix uses a new model oven, the Hybridization Oven 645 (Figure 1.4). If you are using the GeneChip Hybridization Oven 645, refer to the GeneChip Hybridization Oven 645, P/N , for detailed instructions. Figure 1.4 The Affymetrix GeneChip Hybridization 640 (left) and 645 (right) Terminology This user guide makes a distinction among the terms test request, assay, array and array cartridge although many users of the AMDS system employ these terms interchangeably. The test request is a database record of the specimen identification (Specimen ID), the assay parameters (Assay Name) and a unique array cartridge identification number (Array ID), as well as supplementary specimen information. You set this up when you create, or enter, a test request. The specimen assay, which the partner has designed using the assay software module, employs the Affymetrix GeneChip array or the partner manufactured microarray to process the specimen and generate test results. An assay is a procedure, i.e., a collection of steps based on the assay parameters that tell AMDS how to process an array. AMDS also refers to the nucleic acid test sample as the target.

14 12 The AMDS User s Guide Rev. B An array is the physical microarray component that technicians created based on the specimen type and assay parameters. This consists of a glass substrate on which was placed oligonucleotide sequences. A plastic cartridge surrounds and protects the array and forms the array cartridge. We use the term array mainly to refer to the array itself and what AMDS does to the array based on the assay parameters. For example AMDS hybridizes, washes and scans an array based on the assay parameters. We use the term array cartridge to refer to the physical array unit that you handle. The array cartridge is the plastic enclosure (Figure 1.5) that supports and protects the array on the glass chip as it proceeds through the AMDS workflow. For example you carry an array cartridge to a hybridization oven, insert an array cartridge into a fluidics station, or insert an array cartridge into the AutoLoaderDx. For convenience, we also refer to the GeneChip Fluidics Station 450Dx as the fluidics station or as the FS450Dx and the GeneChip Scanner 3000Dx with AutoLoaderDx as the AutoLoaderDx. Figure 1.5 Affymetrix GeneChip array cartridges

15 How This Guide Is Organized chapter 1 Welcome to AMDS 13 Chapter 1 deals with the introduction to the AMDS system. Chapter 2 deals with a more detailed AMDS overview and the concept of workflow. Chapter 3 introduces the AMDS graphic user interface (GUI) and the concept of roles and privileges. Chapter 4 shows you in detail how to process a specimen sample through the AMDS workflow. This is the most important chapter for technicians who will directly run the samples. Chapter 5 introduces you to the AMDS administrative features. This chapter is for those who have administrative privileges. Chapter 6 is a brief chapter on the printing of results and logs. Chapter 7 shows you how to perform basic troubleshooting. Appendix A describes in detail how the Fluidics Station 450Dx works and how to perform basic maintenance. You must read and understand this chapter before attempting to process arrays. Appendix B describes in detail how the AutoLoaderDx works and how to perform basic maintenance. You must read and understand this chapter before attempting to process arrays. Conventions Used in This Guide This manual provides a detailed outline for all tasks associated with AMDS. Various conventions are used throughout the manual to help illustrate the procedures described. Explanations of these conventions are provided below. Instructions for procedures are written in a step format. Immediately following the step number is the action to be performed. Following the response, additional information pertaining to the step may be found and is presented in paragraph format. For example: Click Yes to continue. The task proceeds.

16 14 The AMDS User s Guide Rev. B Text Alerts Text alerts will draw your attention to a particular piece of information. There are five types of text alerts: Note, Tip, Important, Caution and Warning. NOTE: The Note format presents important information pertaining to the text or procedure being outlined. TIP: Information presented in Tips provide helpful advice or shortcuts for completing a task. IMPORTANT: Important notes alert you to information important to the understanding or implication of the procedure or text. CAUTION: Caution notes advise you that the consequence(s) of an action may be irreversible and/or result in lost data. WARNING: Warnings alert you to situations where physical harm to person or damage to hardware is possible.

17 chapter 1 Welcome to AMDS 15 Resources Other Documentation The following quick reference cards are available in various languages. Part Number Quick Reference Card Title Affymetrix Molecular Diagnostic Software AMDS Quick Reference Card, English Affymetrix Molecular Diagnostic Software AMDS Quick Reference Card, French Affymetrix Molecular Diagnostic Software AMDS Quick Reference Card, German Affymetrix Molecular Diagnostic Software AMDS Quick Reference Card, Italian Affymetrix Molecular Diagnostic Software AMDS Quick Reference Card, Spanish Affymetrix Molecular Diagnostic Software AMDS Quick Reference Card, Portuguese Affymetrix Molecular Diagnostic Software AMDS Quick Reference Card, Dutch Affymetrix Molecular Diagnostic Software AMDS Quick Reference Card, Danish Affymetrix Molecular Diagnostic Software AMDS Quick Reference Card, Swedish Affymetrix Molecular Diagnostic Software AMDS Quick Reference Card, Greek Affymetrix Molecular Diagnostic Software AMDS Quick Reference Card, Japanese

18 16 The AMDS User s Guide Rev. B Technical Support If you have questions or require technical support, please contact Affymetrix technical support. If you are experiencing instrument (FS450Dx or AutoLoaderDx) problems, especially under any of the following conditions, unplug the instrument from the power source and contact Affymetrix Technical Support: when the power cord is damaged or frayed; if any liquid has penetrated the instrument; if, after service or calibration, the instrument does not perform to the specifications stated in the section, The FS450Dx Instrument Specifications on page 187 or the section, The AutoLoaderDx Specifications on page 224. If the instrument must be returned for repair, call Affymetrix technical support. IMPORTANT: Make sure you have the model and serial number. Affymetrix, Inc Central Expressway Santa Clara, CA USA support@affymetrix.com Tel: (1-888-DNA-CHIP) Fax: Affymetrix UK Ltd. Voyager, Mercury Park, Wycombe Lane, Wooburn Green, High Wycombe HP10 0HH United Kingdom

19 chapter 1 Welcome to AMDS 17 Tel: +44 (0) Fax: +44 (0) France Tel Germany Tel supporteurope@affymetrix.com Affymetrix Pte. Ltd. (Singapore) 7 Gul Circle Keppel Logistics Building, Level 2M Singapore Tel: (65) Fax: (65)

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21 Chapter2 AMDS OVERVIEW Introduction AMDS provides the ability to process a microarray based on assay parameters. This includes: processing test requests through the AMDS application workflow creating test requests registering test requests hybridizing the array washing and staining the array in a fluidics station scanning the array in the GeneChip AutoLoaderDX creating a test report AMDS also manages the assay workflow: The system provides for: Viewing Logs: the system provides the ability to view logs, both audit and system logs, which record activities performed on the system. See Viewing Logs, on page 102. Assay Management: the system provides the ability to install and deactivate assays. The software manages assays through the worklist management function. See Managing the Assay, on page 105. User Management: this includes creating users and passwords, activating and deactivating users. The system also provides the ability to manage access to the system by associating users with groups. A group defines roles and permissions that control what system functions AMDS allows the user to perform. AMDS can also associate users with assays that AMDS allows them to run. See Managing the Users, on page 109.

22 20 The AMDS User s Guide Rev. B System Management: the system provides the ability to maintain the system, including performing regular maintenance, and performing regular systems checks. See Managing the System, on page 113. Assay Workflow The AMDS automates instrument control and provides a central infrastructure to acquire and track test requests. However, AMDS does not control target preparation. You must refer to the relevant Affymetrix package inserts and other documentation available for specimen handling and target preparation. Table 2.1 shows the major steps and software functions in an assay. Table 2.1 AMDS workflow quick reference guide Assay Step Output Software Function Prepare the target Target registration Hybridize, wash, and stain the array. Prepared sample that you can place onto an array. Associate the target specimen with a unique array type and with reagent lot numbers. Hybridized, washed, and stained target specimen. Performed outside of the AMDS system control. AMDS associates the sample with the reagent used in preparation of the sample as well as with the Array ID. AMDS will then track the test request processing through the workflow to generation of a test report. AMDS tracks the hybridization of the target specimen, which may be performed in a hybridization oven or on the fluidics station, depending on the assay parameters. The system also controls the washing and staining of the target specimen in the fluidics station as defined in the fluidics scripts associated with a particular assay type.

23 chapter 2 AMDS Overview 21 Table 2.1 AMDS workflow quick reference guide (Continued) Assay Step Output Software Function Scan Image data (cell intensity data,.cel file) AMDS automates control of the scanner, acquires and saves the scan data. The system automatically computes and saves the cell intensities from the image data as a.cel file. The system tracks the image and cell intensity data. Run Test Report Test report An Affymetrix or partner created assay module generates test results. AMDS provides a workflow-based tracking system for the data. The worklist manager (see the section, Workflows and Worklists, on page 29) tracks test request status through a series of steps that includes: Registration Hybridization Fluidics washing Scanning Test report generation You can easily confirm the status of a test request that has not been purged from the system. See the section, Archiving Test Requests, on page 121 for information on archiving and purging test requests. Active test requests, those that have not completed all steps of processing, will appear in the Active Worklist. See the section, Active Worklist, on page 32 for more information on Active Worklists. Completed or cancelled test requests that have not yet been purged from the system, will appear on the Non-Active Worklist (See the section, Non-Active Worklist, on page 38 for more information on Non-Active Worklists). Description of Assay Workflow Steps AMDS controls the processing of arrays through a series of workflow steps. This section provides a brief outline of the workflow steps.

24 22 The AMDS User s Guide Rev. B Preparing The Target Sample Refer to the appropriate assay package insert for documentation relevant to preparing your particular specimen for placement on the specific array that contains the assay. Creating, Editing and Deleting the Test Request Before you can process a specimen on AMDS, you must create a test request (TR) in the system. You manually create the test request using the Create Test Request function within the Active Worklist in AMDS. The test request will have a Specimen ID, which identifies the patient s specimen, and the name of the assay type that AMDS will process (Assay Name). AMDS will create a TestRequestID and manage the assay using this ID. You can view, but not edit, the TestRequestID. Before you submit the test request to the registration workflow you will have the opportunity to edit or discard the test request. However, after you have created the test request, you will have the opportunity to edit or cancel it. See the section, Creating, Editing and Cancelling Test Requests The Active Worklist, on page 60 for more information on creating, editing and cancelling test requests. Registering the Test Request Once you have created a test request, the next step in the workflow is registration. The registration step is where you associate the test request with a specific and unique array cartridge (Array ID). The array ID identifies the unique ID of a physical array that comprises the array cartridge. You can use an array cartridge only once for each assay since you can only apply one specimen to a particular array cartridge. As mentioned earlier, you must load, or place, the patient s specimen (called the target) onto the array cartridge, and this occurs outside of AMDS. You can record the placement of the target onto the array cartridge in the registration step. You can also record the Target Preparation Reagent Lot Number used in preparing the target.

25 chapter 2 AMDS Overview 23 The assay type will determine if the system requires the reagent lot number. If the system requires the reagent lot number, you must enter it in addition to the array ID in order to progress to the hybridization step. The registration process associates the specimen s unique ID (Specimen ID) and the unique array ID (Array ID). From that point on, AMDS tracks the specimen using the Array ID throughout the remaining workflow. The assay type, identified by the Assay Name, determines the assay specific steps through which AMDS processes the target (e.g. hybridization, fluidics, scanning, assay reporting), as well as the specific protocols to be used in the individual steps. The target will usually have a barcode associated with it, in which case you can identify the sample by scanning the target barcode. Alternatively, you can enter manually the identifiers for the target, reagent, and array. The test request that you create now contains all the information for processing the specimen on the array. See the section, Registering a Test Request, on page 71 for more information on registering test requests. Hybridizing the Test Request Assay You can hybridize the array that contains the assay specimen in a incubation, or hybridization, oven or on the fluidics station depending on the specifications of the assay (contained in the Assay Name) being performed. During hybridization, you incubate the array with a hybridization cocktail containing the labeled target (the specimen sample) and control oligonucleotides in a buffer optimized for each type of assay performed (refer to the appropriate array package insert for details on the buffers). If you perform hybridization in an Affymetrix hybridization oven, you must place the arrays in a tray (a maximum of 8 arrays to a tray) and load the tray in the hybridization oven at the temperature and for the duration specified by the assay being performed. AMDS manages the hybridization in the hybridization oven by using a separate workflow step with a separate worklist.

26 24 The AMDS User s Guide Rev. B When the system completes the assay, you can remove the array to the fluidics station for washing and staining. If your system is connected to the new Affymetrix Hybridization Oven 645, the system monitors the oven temperature and duration during the hybridization process. For detailed information on using the Affymetrix Hybridization Oven 645, see the Affymetrix Hybridization Oven 645 User s Guide, P/N and the Affymetrix Hybridization Oven 645 Quick Reference Card, P/N If you carry out hybridization in the fluidics station, the fluidics station repeatedly fills and drains the array with the hybridization cocktail. See the section, Hybridizing an Array, on page 76 for more information on hybridizing test requests. Washing and Staining the Array in the Fluidics Station After hybridization, the array undergoes a series of stringent washes (specifically optimized for each type of assay in the fluidics station). If you had labeled the target with a fluorescent tag, you can scan the array at this point using the Affymetrix GeneChip AutoLoaderDx. AMDS controls the fluidics station using pre-programmed fluidics protocols, called scripts, for hybridizing (if necessary), washing, and staining the arrays. A fluidics station contains four modules and each module can process an array using different fluidics protocols. However, each array within a particular fluidics station must be of the same assay type, i.e., the assay should have the same Assay Name. This is because the arrays of the same assay type use the same materials with which the fluidics station has been configured and primed. See the section, Washing and Staining an Array in the Fluidics Station, on page 81 for more information on washing and staining arrays. See also the appendix, The Fluidics Station 450Dx, on page 135 for details on fluidics station use.

27 chapter 2 AMDS Overview 25 Scanning the Test Request Assay the AutoLoaderDx After you have hybridized, washed, and/or stained an array, you can now scan the array that contains the assay. AMDS automates control of the AutoLoaderDx and uses the assay information (stored in the Assay Name file) to manage the scanner settings for each type of assay. The software enables you to start a scan and collect intensity data. After the AutoLoaderDx completes the scan, AMDS creates the raw data for computing intensities. See the section, Scanning an Array, on page 85 for more information on scanning arrays. See also the appendix, The Scanner 3000Dx with AutoLoaderDx, on page 195 for details on the AutoLoaderDx use. If you have administrative privileges, you can use the AutoLoaderDx in three modes: Automode allows you to automate the scanning of arrays by placing up to 48 arrays in a carousel. This is the default operating mode. See the section, Configuring the AutoLoaderDx, on page 213. Manual Mode if you want to disable the automated feature of the AutoLoaderDx (Automode) and scan arrays one by one. See the section, Enable Manual Mode, on page 214. AutoLoaderDx Disabled allows you to use the software alone without the presence of the AutoLoaderDx. See the section, Disable AutoLoaderDx, on page 214. Computing Cell Intensities After the AutoLoaderDx completes the scan, AMDS calculates intensities and produces an array image file, called the.cel file. The strongest hybridization occurs between the particular array oligonucleotide sequence in the specimen target that is most nearly complementary to the immobilized oligonucleotide probe sequence. This produces the strongest fluorescence intensity.

28 26 The AMDS User s Guide Rev. B The software represents the fluorescence intensity values from each pixel on the array in a grayscale or pseudo-color mode and superimposes a grid on the image to delineate the probe cells (features). AMDS automatically: Analyzes the image data and computes a single intensity value for each probe cell on an array. Saves the cell intensity data as a.cel file. Outputs the.cel file to an archive folder. Displaying and Archiving Test Results At the end of the assay procedure, you can see the results by clicking the Awaiting Review hyperlink in the Review Results field in the Active Worklist window. A window will appear that allows you to review and either accept the results or, if there is an obvious error, reject the results. The particular format of the test results will depend on the design of the partner s results display. See the section, Reviewing Test Results, on page 89 for more in formation on viewing results.

29 Chapter3 AMDS USER INTERFACE AND WORKFLOW Introduction This chapter explains the AMDS user interface and workflow concept of AMDS. The workflow of AMDS starts with the creation of a test request and ends with the production and communication of a test result. NOTE: The particular form of the communication of the test result will depend on the design of the partner s assay and software application. This chapter also introduces you to running an assay in AMDS. This means creating and processing test requests. AMDS maintains worklists to track all test requests in the system. Once you enter test requests into the system and associate them with arrays, the system processes the arrays through the various workflow steps, such as target registration, hybridization, fluidics, scanning, and assay report generation, in order to generate test results.

30 28 The AMDS User s Guide Rev. B The AMDS Application Worklists comprise the AMDS application. Worklists provide control for the various functions: test request creation, editing and registration, as well as array hybridization, washing and staining, and scanning. AMDS also includes several other essential functions such as logging, system management, and system maintenance. In summary, the AMDS application provides you with the following functions: System Access Log On User Interface Log Off Worklist Management Active Worklist Enter Test Request Non-Active Worklist Test Request Management Edit Test Request Cancel Test Request Workflow Processing Registration Hybridization Oven Fluidics Scanner Review Results Administrator User Management System Management Assay Management View Logs The AMDS User Interface After you successfully log on, the main AMDS user interface appears. Three regions comprise this main interface: Left hand region provides workflow and worklist navigation and administrator features. Center region displays lists of test requests that AMDS is running. Thus, for example, when AMDS performs a fluidics protocol the center region displays a list test requests that are at the fluidics stage of their processing. Right hand region contains user and instrument status information. Figure 3.1 shows the functionality provided by each region.

31 chapter 3 AMDS User Interface and Workflow 29 Center Panel Left Panel Right Panel Figure 3.1 The AMDS user interface Workflows and Worklists The worklists manage test requests in the workflows. The Active Worklist and Non-Active Worklist monitor the flow of the test request through the AMDS system. Various menus display the status of each test request. Worklist functions include the ability to view the Active worklists and to enter new test requests manually. The Left Panel The Workflow The left panel is the workflow panel. The workflow panel provides icons that allow you to navigate through the workflow steps for processing a test request and array. The left panel provides access to both the workflow and administrator functions (Figure 3.2).

32 30 The AMDS User s Guide Rev. B Figure 3.2 Workflow management pane

33 chapter 3 AMDS User Interface and Workflow 31 The Center Panel The Worklists The center region contains a worklist panel which lists, within the system, all the test requests that meet the criteria for that test. This region displays a worklist that is relevant to the function invoked. Active Worklist all test requests that are active and waiting for you to further process them Registration Worklist all test requests for which you have associated an array ID Hybridization Worklist all test requests that are undergoing or about to undergo hybridization Fluidics Worklist all test requests that are undergoing or about to undergo hybridization, washing and/or staining in the fluidics station Scanner Worklist all test requests that are undergoing or about to undergo scanning in the AutoLoaderDx Non-Active Worklist all test request that you have completed or cancelled

34 32 The AMDS User s Guide Rev. B Active Worklist The active worklist (Figure 3.3) displays all test requests the AMDS is currently processing. The worklist indicates the current stage in the workflow for each active test request. You cannot directly edit this list; rather the system maintains and updates this list. See the section, Managing Test Requests, on page 60 for more details about the active worklist and creating test requests. Figure 3.3 The Active Worklist button

35 Registration Worklist chapter 3 AMDS User Interface and Workflow 33 The registration worklist (Figure 3.4) allows you to associate a single array cartridge with the test request and add, if necessary, target preparation reagent lot numbers as well as add any comments. See the section, Processing Test Requests, on page 75 for more details about registration. Figure 3.4 The Registration Worklist window

36 34 The AMDS User s Guide Rev. B Hybridization Worklist The hybridization worklist (Figure 3.5) allows you to associate hybridization oven information with the test request and add any comments desired. See the section, Hybridizing an Array, on page 76 for more details about hybridization. You can supply your own oven. If you are using the GeneChip Hybridization Oven 645, refer to the Hybridization Oven 645 User s Guide (P/N ). Figure 3.5 The Hybridization Worklist

37 Fluidics Worklist chapter 3 AMDS User Interface and Workflow 35 The fluidics worklist (Figure 3.6) allows you to associate a fluidics station and module with the test request. This particular fluidics station will be the one that will wash and stain the array. You may add comments. The fluidics worklist window will appear the same whether the system processes a test request using the hybridization oven or the fluidics station. See the section, Washing and Staining an Array in the Fluidics Station, on page 81 and the appendix, The Fluidics Station 450Dx, on page 135 for more details on using the Fluidics Station 450Dx. Figure 3.6 The Fluidics Worklist

38 36 The AMDS User s Guide Rev. B Scanner Worklist The scanner worklist (Figure 3.7) allows you to associate a test request with the AutoLoaderDx for the scanning of the array. You may add comments. See the section, Scanning an Array, on page 85 and the appendix, The Scanner 3000Dx with AutoLoaderDx, on page 195 for details on scanning using the AutoLoaderDx. Figure 3.7 The Scanner Worklist

39 Reviewing Test Results chapter 3 AMDS User Interface and Workflow 37 The review results display (Figure 3.8) allows you to review and approve or reject the results of the assay that AMDS just processed. You can access a report by clicking on the hyperlink, Awaiting Review, on the Active Worklist, Review Results field. See the section, Reviewing Test Results, on page 89 for details on viewing test results. Figure 3.8 The Review Results Function

40 38 The AMDS User s Guide Rev. B Non-Active Worklist This non-active worklist (Figure 3.9) displays the non-active test requests in the system. The system moves test requests to the Non- Active Worklist either when you cancel them, or when you view them in the Review Results step. Figure 3.9 The Non Active Worklist

41 chapter 3 AMDS User Interface and Workflow 39 The Right Panel User and Instrument Details The right panel, or region (Figure 3.10), provides important details necessary to monitor the user and instrument operation. Figure 3.10 The right panel pane

42 40 The AMDS User s Guide Rev. B User Details The upper portion of the right hand region contains the User Details panel (Figure 3.11). This panel displays information regarding the user that is currently logged on to the AMDS. It also provides the means for logging off of the AMDS, and shutting down the system. Figure 3.11 The User Details panel Device Status Below the User Details panel is the Device Status panel (Figure 3.12). This panel displays information regarding the status of the instruments in the form of a dashboard. green indicates that the instrument is operating normally yellow indicates that AMDS detects an abnormal condition and has raised an alert that needs attention red indicates a failure for that instrument AMDS will monitor and report the status of the Hybridization Oven 645 (if connected), the fluidics station, the printer and AutoLoaderDx.

43 Figure 3.12 Device Status, Alerts, Alert Details panels chapter 3 AMDS User Interface and Workflow 41

44 42 The AMDS User s Guide Rev. B Alerts Below the Device Status panel is the Current Alerts panel, which displays all system alerts (Figure 3.12). This may include notification that a problem occurred in processing which needs attention (e.g. the fluidics station is out of wash buffer). Alert Details and Recommended Resolution This panel gives you details of the particular alert and suggestions on dealing with that alert (Figure 3.12). Since the alert details can change based on the version of AMDS, it is not possible to list all the various messages that comprise the individual alert details. If an alert occurs you should read the detailed description and follow the recommended solution. See also the chapter, AMDS Troubleshooting, on page 127 for details on device troubleshooting. Roles and Privileges AMDS provides users with various levels of control. The laboratory supervisor or system maintainer can assign these roles to the users. This section provides a brief summary of the various roles and privileges. Everybody can at the minimal level of privileges: Log on Log off Change their password View all worklists View Assay Management screen Guests also can do this minimal level. Technicians can do the minimal level and, and in addition, can also, for all approved and registered assays: Enter/Edit/Cancel test requests Process test requests through the workflow (stopping short of approving/rejecting the result) View assay GUI Resolve alerts

45 chapter 3 AMDS User Interface and Workflow 43 View System Logs A Technologist have the ability to: Shut down the system Approve/Reject results (for all approved and registered assays) The System Maintainers can: Perform user management Perform assay management Archive and purge data Perform user service on the instruments Perform general configuration of the system The laboratory supervisor can do anything that the technologist can do in addition to anything the system maintainer can do. The Administrator Panel The lower section of the left hand region contains the Administrator panel (Figure 3.13). See the chapter, The AMDS Administrative Features, on page 95 for details on using the administrator functions. The Administrator buttons give you the capabilities to view system and audit logs (View Logs), install and deactivate assay modules (Assay Management), add and manage users of the system (User Management), and manage instrument and other aspects of the system (System Management). This chapter describes each of these functions.

46 44 The AMDS User s Guide Rev. B Administrator Functions When you click on an administrative function (Figure 3.13), the center window will open and display additional detail regarding the selected administrative function. If you do not have administrative permissions, you will not see the Administrator panel. Figure 3.13 Administrative function buttons View Logs select a system log or an audit log to filter, view, print, or export. The audit logs can be a workflow step (hybridization, fluidics, scan) or report type (information or error type) or user type. See the section, Viewing Logs, on page 102. Assay Management select an assay to install, activate or deactivate. See the section, Managing the Assay, on page 105. User Management add or remove users or select a user to change the user s permissions or passwords. See the section, Managing the Users, on page 109. System Management gain access to the In-House Services function to make changes to the Fluidics Station and workstation settings, archive test requests, view instrument service logs, and set the general configuration. See the section, Managing the System, on page 113.

47 Chapter4 TEST REQUEST PROCESSING Introduction This chapter shows you how to process test requests through the various steps of the workflow in AMDS. IMPORTANT: Before attempting any assay runs, you must be familiar with the operation of the fluidics station (see the appendix, The Fluidics Station 450Dx, on page 135) and the operation of the AutoLoaderDx (see the appendix, The Scanner 3000Dx with AutoLoaderDx, on page 195). AMDS Quick Reference Guide The AMDS quick reference guide summarizes the various tasks and how to perform them in the various worklist panels (Table 4.1). Table 4.1 AMDS Quick Reference Guide for the Workflow If you want to: Create a test request Then do this in a Worklist panel: 1. If not already in the Active Worklist window, click the Active Worklist button. 2. Click the Create button. 3. Complete the required fields. Specimen ID Assay Name 4. Click the Submit button.

48 46 The AMDS User s Guide Rev. B Table 4.1 AMDS Quick Reference Guide for the Workflow (Continued) If you want to: Delete a new test request (if you have not yet submitted a test request) Edit a test request Cancel a test request (after you have submitted that test request) Associate various reagent lot numbers to a batch of test requests assay batch Then do this in a Worklist panel: 1. If not already in the Active Worklist window, click the Active Worklist button to open the Active Worklist window. 2. Click the Create button. 3. Select the test request that you have just entered but have not yet submitted. 4. Click the Delete button. Note: you cannot delete the request after you have clicked the Submit button; you must cancel test request. 1. If not already in the Active Worklist window, click the Active Worklist button. 2. Select the test request. 3. Click the Edit button. 4. Change the following fields Specimen ID Assay Name 5. Click the Save button. 1. If not already in the Active Worklist window, click the Active Worklist button. 2. Select the test request. 3. Click the Cancel Test Request button. 1. In any worklist, select one or several Target Request records WITH THE SAME ASSAY NAME. 2. Click the Assay Batch button. 3. Fill in (if necessary) the Target Prep Reagent Lot Number. 4. Fill in (if necessary) the Reagent Lot Number. 5. Fill in (if necessary) the Hybridization Reagent Lot Number. 6. Click OK. 7. Confirm Step: enter your user name and password. 8. Click OK.

49 chapter 4 Test Request Processing 47 Table 4.1 AMDS Quick Reference Guide for the Workflow (Continued) If you want to: Register a test request Set up test requests for hybridization Then do this in a Worklist panel: 1. Click the Registration button to open the Registration worklist. 2. Select the test request. 3. Complete the following fields Array ID (scan the cartridge array barcode or enter manually) Reagent Lot Number optional (scan the barcode of the reagent kit or enter manually) 4. Click the Save button. 5. Click the Complete Step button. 1. Click the Hybridization Oven button to open the Hybridization Worklist. 2. Select the test requests. 3. (Optional: Click the Select Tray button and enter the oven number or E if you are using an external, or unconnected, oven). 4. Associate the test requests with that tray. 5. Click the Start button. 6. Click the End button (when hybridization is complete). 7. Click the Complete Step button.

50 48 The AMDS User s Guide Rev. B Table 4.1 AMDS Quick Reference Guide for the Workflow (Continued) If you want to: Set up a fluidics station or shut down a fluidics station Then do this in a Worklist panel: 1. Click the Fluidics button to open the Fluidics Worklist. 2. Click the Fluidics Station Setup button. 3. Select the assay for a particular Fluidics Station number 4. Enter the particular Wash A and Wash B for each fluidics station. 5. Select the modules to run the fluidics station protocols. 6. Add comments. 7. Click the Close button if you want to reject the changes. 8. Click the Save button if you want to accept the changes. 9. Click the Shut Down button to shut down the Fluidics Station. Prime a fluidics station 1. Add the proper reagent wash buffers and 1.5 ml vials in accordance with the assay protocol instructions. 1. Click the Fluidics button to open the Fluidics Worklist. 2. Click the Station Setup button to go to the setup window. 3. Select the row containing the fluidics station to prime. 4. Click the Prime Fluidics Station button. 5. Enter the Fluidics Station: Number Module 6. Click the Start button.

51 chapter 4 Test Request Processing 49 Table 4.1 AMDS Quick Reference Guide for the Workflow (Continued) If you want to: Set up test requests for a fluidics protocol Set up test requests for scanning Then do this in a Worklist panel: 1. Click the Fluidics button to open the Fluidics Worklist. 2. VIEW THE PROMPTS ON THE FLUIDICS STATION LCD FOR INSTRUCTIONS: Add the proper reagent wash buffers and 1.5 ml vials in accordance with the assay protocol instructions. 3. VIEW THE PROMPTS ON THE FLUIDICS STATION LCD FOR INSTRUCTIONS: Insert the arrays into the fluidics station modules. 4. If you do not have a barcode reader: a. Select the test requests b. Enter the Station # c. Enter the Module # 5. If you have a barcode reader: a. Scan the array barcode b. Scan the fluidics module barcode 6. Click the Start button. 7. Click the Complete Step button (when the fluidics protocol is complete). 1. Insert your arrays into the AutoLoaderDx 2. Click the Scanner button to open the Scanner Worklist. 3. Click the Scan button (no need to select arrays). 4. Click the Complete Step button (when the scan is complete).

52 50 The AMDS User s Guide Rev. B Table 4.1 AMDS Quick Reference Guide for the Workflow (Continued) If you want to: Scan arrays in the Manual Scan mode Review results Then do this in a Worklist panel: 1. Insert the array into slot #1 of the AutoLoaderDx carousel. 2. Click the Scanner button to open the Scanner Worklist. 3. Select the test request. 4. Add identifying information for each test request if necessary. 5. Click the Manual Scan button. 6. Click the Complete Step button (when the scan is complete). 1. Click the Active Worklist button. 2. Click the Awaiting Review hyperlink. 3. View the Test Results Report. 4. Add comments. 5. Click the Print button if you want to print the report. 6. Click the Approve button to approve the report. 7. Click the Reject button to reject the results. 8. Fill in your user name and password.

53 chapter 4 Test Request Processing 51 Using the Barcode Reader You can use the barcode reader to: Enter a specimen ID for a test request Associate a test request with an array ID Associate a test request with reagent lot numbers Associate multiple test requests with a reagent lot number (assay batch) Associate an array with a fluidics station and fluidics station module that is performing the run. As an example, in the AMDS Registration window, for each test request, you can associate the Specimen ID, Array ID, and Reagent Lot # together by scanning the barcodes affixed to each item. In the fluidics station, you do not need to select manually test requests prior to running a fluidics protocol. Just scan the array barcode then immediately scan the fluidics station module barcode. AMDS will automatically place the information in the proper test results fields (Figure 4.1). Array Barcode Module Barcode Figure 4.1 Using the barcode reader to scan an array barcode and a module barcode

54 52 The AMDS User s Guide Rev. B See the section, Using the Barcode Reader with the Fluidics Station, on page 142 for more information on using the barcode reader with the fluidics station. The following additional examples will help familiarize you with how to use the barcode reader in AMDS: Within the Registration Worklist screen, highlight the desired test request record and use the barcode reader to read the barcode affixed to the array cartridge. AMDS will locate the proper field and automatically fill it in with the proper identification number. For information regarding connecting the barcode reader, see the section, Connecting the Barcode Reader, on page 203. NOTE: Note: Alternatively, if the barcode on any item is not readable for any reason, you can manually enter the ID by typing the number into the field after positioning the cursor in that field, rather than scanning the barcode. Handling the Array Cartridge The array comes mounted in a plastic package to form an array cartridge (Figure 4.2). The array contains a collection of oligonucleotide probes that have been arrayed on the inner glass surface. A chamber in the plastic package directly under the chip acts as a reservoir where hybridization and washing/staining occur. Figure 4.2 The array cartridge

55 chapter 4 Test Request Processing 53 Although the inner glass surface is protected, any contamination or scratches on the outer surface of the glass can compromise the integrity of the scan. Avoid touching the surface of the chip with your fingers. Skin oils and other substances, such as lotions or ink, can fluoresce. If the surface of the array chip is noticeably dirty, you should carefully clean the chip with a nonabrasive laboratory tissue.

56 54 The AMDS User s Guide Rev. B Starting AMDS IMPORTANT: Shutting down the AutoLoaderDx: to preserve the lifetime of the scanner's internal laser we recommend that you turn the AutoLoader OFF when it is not in use for any extended period of time such as overnight or a weekend. Turning on the System 1. Turn on the computer workstation to launch AMDS. If you had administrator privileges, and had earlier selected the option Turn AutoLoaderDx on at AMDS launch, then the laser will start to warm up when you launch AMDS. If you have administrator privileges, see the section, Managing the AutoLoaderDx, on page 124 for instructions on how to do this. AMDS will perform a system self test to confirm the operational status of the system and ensure that all components are connected and operating properly. 2. Once AMDS completes a self test, the AMDS User Logon screen will appear (Figure 4.3).

57 chapter 4 Test Request Processing 55 Figure 4.3 User Logon Screen 3. Log on to AMDS by entering your User Name and Password (provided by the Affymetrix service technician who installed AMDS or your system administrator) and click the Log On button. AMDS will authenticate your user name and password provided and present the initial system screen, shown in the following section: AMDS user interface. The system will provide access to the appropriate system functionality based on your user group with which you are associated. For details on user groups and permissions refer to the section, The AMDS Administrative Features, on page Turn on the AutoLoaderDx (for more detail on starting the AutoLoaderDx, see the section, Starting the AutoLoaderDx, on page 212). 5. Turn on the Affymetrix Fluidics Station 450Dx (for more detail on starting the fluidics station, see the section, Operating the Fluidics Station, on page 145).

58 56 The AMDS User s Guide Rev. B WARNING: Laser in use during scanning. NOTE: The scanner laser should be turned on and warmed up for at least 10 minutes.

59 Changing Your Password chapter 4 Test Request Processing 57 You can change your password from any workflow window. 1. In the User Details panel on any workflow window (Figure 4.4), click the Change Password button. Figure 4.4 The User Details panel The Change Password dialog box opens (Figure 4.5).

60 58 The AMDS User s Guide Rev. B Figure 4.5 The Change Password dialog box 2. Enter you old password. 3. Enter your new password. 4. Confirm you new password by entering it again. 5. Once you enter your information, click the OK button to apply the change. Logging Off This function allows you to log off of the AMDS. The log off functionality is available at all times. 1. In the User Details panel on any workflow window (Figure 4.4), click the Log Off button. Logging off will not terminate the active workflow processes. If there are test requests in hybridization, fluidics or scanning, AMDS will continue to process them.

61 chapter 4 Test Request Processing 59 Shutting Down This function allows you to shut down AMDS. The shut down functionality is available at all times. 1. In the User Details panel on any workflow window (Figure 4.4), click the Shut Down button. A System Shutdown message appears asking if you are sure you want to shut down. Click Yes or No. 2. A confirm window appears. Fill in your user name and password. Click Yes. The system will wait until AMDS completes all currently running test requests and then shut down. The system will not shut down if there are test requests in progress or complete on any worklist. In this situation, either wait for the test requests to finish or cancel the test requests.

62 60 The AMDS User s Guide Rev. B Managing Test Requests This section shows you how to enter, edit and cancel a test request using the AMDS workflow. This involves using the active worklist to create or edit the test request data and the registration worklist to associate the test request with a unique, physical, array cartridge ID. Creating, Editing and Cancelling Test Requests The Active Worklist You can create, edit and cancel test requests. In addition, you can also filter, select all or assay batch the worklists. The Active Worklist panel provides these functions (Figure 4.6). The following flow chart summarizes the steps required in creating or editing a test request. Active Worklist Create Add Specimen ID & Assay Name Enter Assay Batch information for a number of related test requests Submit Figure 4.6 The Active Worklist button

63 chapter 4 Test Request Processing 61 Creating the Test Request 1. If you are not already in the Active Worklist window, select Active Worklist from the left pane (Figure 4.6). The Active Worklist panel opens (Figure 4.7). Figure 4.7 The Active Worklist 2. Click the Create button on the toolbar of the Active Worklist. The Enter Test Request Screen will appear (Figure 4.8).

64 62 The AMDS User s Guide Rev. B Figure 4.8 The Enter Test Request window 3. Enter one or more Specimen ID and Assay Name combinations. 4. Once you have made the entries, click the Submit button and the Enter Test Request screen closes. Adding Additional Information to the Specimen ID After you add a specimen, and return to the Active Worklist window, you can add certain types of pertinent information about the specimen. You can also add this information at a later date in other worklist windows. 1. Click on the desired Specimen ID The Additional Information dialog box opens (Figure 4.9). 2. Add the following information. This this information includes: - Patient First Name - Patient Last Name - Patient ID - Specimen Type - Tissue - Specimen Type - Tissue Subtype

65 chapter 4 Test Request Processing 63 - Specimen Type - Collection - Specimen Type - Storage Processing - Special Specimen Type - Collection Date - Collection Time - Requesting Physician First Name - Requesting Physician Last Name - Requesting Institution 3. When you have completed adding the information, click Save and Close or just Close to exit without saving. Figure 4.9 The Specimen ID additional information dialog box Retrieving Additional Information and Viewing Test Request Logs You can retrieve a summary of all the specimen information and test request logs for particular assay type.

66 64 The AMDS User s Guide Rev. B 1. In the Assay Name field, click on the Assay Name. The Assay Home (aka Assay Landing) window appears (Figure 4.11). Figure 4.10 The Test Request Log tab 2. Click on the Specimen Report tab to view all the specimen IDs associated with that assay type. 3. Click on the Test Request Log tab (Figure 4.11) to view all the test requests associated with that assay type. Each test request will include information on its: - Date - Time - User - Type - Sub System - Short Message

67 chapter 4 Test Request Processing 65 Figure 4.11 The Test Request Log tab Editing Test Requests This function allows you to edit a test request. You can edit test requests before you submit them, that is, before they enter the registration stage. You cannot edit test requests after the system completes registration. Editing the Test Request Procedure 1. From the Active Worklist, select a test request to be edited. 2. Click the Edit button on the toolbar of the Active Worklist panel. The Edit Test Request panel will appear (Figure 4.12).

68 66 The AMDS User s Guide Rev. B Figure 4.12 The Edit Test Request window 3. Modify either the Specimen ID or Assay Name (these are the only two fields that you can edit). 4. Click the Save button. 5. The Confirm Step dialog box appears (Figure 4.13). 6. Enter your User Name and Password and an Event Reason as well as any other information in the Additional Info box. 7. If you want to cancel the edit and return to the Active Worklist, click the Cancel Edit button. 8. If you want to discard the edits but remain in the Edit Test Request screen, click the Discard Changes button.

69 chapter 4 Test Request Processing 67 Figure 4.13 The Confirm Step dialog box Deleting Test Requests You can delete a test request if you have not yet submitted it to the worklist. 1. If you are not already in the Active Worklist window, select Active Worklist from the left pane (Figure 4.6). The Active Worklist panel opens (Figure 4.7). 2. Click the Create button on the toolbar of the Active Worklist. The Enter Test Request Screen will appear (Figure 4.8). 3. Select the test request that you want to delete and click the Delete button. AMDS will immediately delete the contents of the test request record.

70 68 The AMDS User s Guide Rev. B Cancelling Test Requests After you have submitted a test request, you cannot delete it, but you can cancel it and send it to the Non-Active Worklist. 1. From the Active Worklist, select the test request you would like to cancel. 2. Click the Cancel Test Request button on the toolbar of the Active Worklist panel. The Confirm Step dialog box appears (Figure 4.14). 3. Enter your User Name and Password and an Event Reason as well as any other information in the Additional Info box. Figure 4.14 The Confirm Step dialog box 4. AMDS will transfer the test request to the Non-Active Worklist (Figure 4.15).

71 Figure 4.15 The Non Active Worklist chapter 4 Test Request Processing 69

72 70 The AMDS User s Guide Rev. B Associating Reagent Lot Numbers to Multiple Test Requests Assay Batch You can use the Assay Batch command to associate certain reagent lot numbers to multiple test request records. These lot numbers include target preparation reagent lot numbers, stain reagent lot numbers and hybridization reagent lot numbers. 1. From the Active Worklist or Registration Worklist, select one or more test requests or, if all the test requests use the same Assay Name, click the Select All button to select all the listed test requests. IMPORTANT: The Select All button will only work if all the test requests are associated with one Assay Name. 2. Click the Assay Batch button. The Assay Batch Information dialog box appears (Figure 4.16) The right column lists the selected Specimen IDs The left dialog box allows you to enter: - Target Prep Reagent Lot Number - Stain Reagent Lot Number - Hybridization Reagent Lot Number 3. Click the Save and Close button to save and close, or the Close button to close without saving.

73 chapter 4 Test Request Processing 71 Figure 4.16 The Assay Batch Information dialog box Registering a Test Request The following flow chart summarizes the steps required in registering a test request. The steps in bold are those relevant to the registration procedure. Active Worklist Create Add Specimen ID & Assay Name Submit Register Add Array ID (and Reagent Lot Number) Save Complete Step

74 72 The AMDS User s Guide Rev. B Figure 4.17 The Registration Worklist button Registration Procedure 1. Click the Registration button from the workflow window (Figure 4.17). The Registration Worklist will appear in the center panel (Figure 4.18).

75 chapter 4 Test Request Processing 73 Figure 4.18 The Registration Worklist window 2. Highlight the desired test request record and scan the barcode on the array cartridge. Or scan the specimen ID barcode and then scan the barcode on the array cartridge. The AMDS will locate the proper field and add the info. If you are manually entering information, click in the Array ID field and manually enter the appropriate array ID barcode the array. 3. Optional: If you want to enter reagent lot numbers: Select one or more test requests and enter the same reagent lot number for all these test requests by scanning the barcode on the reagent kit. If you are manually entering information, Shift-click and select all the test requests. Select one Reagent Lot Number field of a test request, enter the value manually, click Enter and AMDS will fill in all the selected test requests.

76 74 The AMDS User s Guide Rev. B 4. When you enter text information in the field in question (Array ID and Reagent Lot Number) AMDS will check your information. If a problem exists, you will get one of the following error messages. You must correct the error before AMDS will proceed. - If that Array ID already exists, AMDS will alert you with an error message. - If you have entered an invalid part number, AMDS will alert you with an error message. - If the array has expired, AMDS will alert you with a warning message. - If any test requests have an invalid array ID, AMDS will alert you with an error message. 5. Click Save button to save your registration and remain in the registration field. 6. Click the Complete Step button to move the test requests with complete information from the Target Registration Worklist to the next step in the workflow. The particular assay being run will determine the next step. This may be the Hybridization Oven step or the Fluidics step.

77 Processing Test Requests chapter 4 Test Request Processing 75 From this point on, you will be processing an array. This section describes the physical steps involved in processing an array, from hybridizing the array to producing a test report. The particular assay that you are running determines the specific sequence of steps required to process the array. For example, an assay may specify that the you must hybridize an array in a hybridization oven. In this case, the system will process the array through the hybridization oven step. Alternatively, the assay may call for AMDS to hybridize an array in the fluidics station. In this case, the system will bypass the hybridization oven step and process the array in the fluidics station after you have registered the sample. See the section, Washing and Staining an Array in the Fluidics Station, on page 81 and the appendix, The Fluidics Station 450Dx, on page 135. The workflow processing described in this chapter presents the possible steps in which an assay may participate and does not imply that a particular assay will participate in all of the steps.

78 76 The AMDS User s Guide Rev. B Hybridizing an Array The following flow chart summarizes the steps required to process an array from test request creation to the end of the array hybridization protocol. The steps in bold are those relevant to the hybridization procedure. This procedure assumes that your workstation is connected to the Affymetrix Hybridization Oven 645. Active Worklist Create Add Specimen ID & Assay Name Submit Register Add Array ID Save Complete Step Hybridization Select Tray # (optional) & Select Oven #Start End Complete Step If you are using the GeneChip Hybridization Oven 640, refer to the GeneChip Hybridization Oven 640 User s Guide, P/N , for detailed instructions. If you are using the GeneChip Hybridization Oven 645, refer to the GeneChip Hybridization Oven 645, P/N , for detailed instructions. IMPORTANT: If you are using the Hybridization Oven 645, you must manually enter the oven number. If you are not using or connected to the Hybridization Oven 645, you should also manually enter the Tray # (optional) and Oven # before starting the hybridization incubation.

79 chapter 4 Test Request Processing 77 Figure 4.19 The Hybridization Worklist button Hybridization Oven Procedure 1. Click the Hybridization Oven button from the workflow (Figure 4.19). The Hybridization Oven Worklist appears. (Figure 4.20). NOTE: You cannot change any parameter in the Time/Rotation/Duration field. Technicians set these when they originally designed the particular assay.

80 78 The AMDS User s Guide Rev. B Figure 4.20 The Hybridization Worklist 2. Associate test requests with a particular tray. a. Shft-click or Ctl-click to select several test requests b. Ctl-click in the tray# field. c. Enter the tray number. d. Press Enter. AMDS will associate all the selected test requests with the tray number. e. If you want to select all the test requests that were earlier associated with a particular tray, select one test request with the newly added tray number and click the Select Tray button. All the test requests associated with that tray will be selected. 3. Associate test requests with a particular oven. a. Shft-click or Ctl-click to select several test requests b. Ctl-click in the oven# field.

81 chapter 4 Test Request Processing 79 c. Enter the oven number. If you are using the Hybridization Oven 645, this number may be either 1 or 2 depending on your oven configuration. d. Press Enter. AMDS will associate all the selected test requests with the oven number. NOTE: If you are using a third party oven or the GeneChip Hybridization 640, enter E for external in the Oven # field. 4. Select one or more test requests. All test requests run at the same time in the same oven must have the same required temperature, rotation and duration). 5. Place the array cartridges in the in the tray then in the oven. Refer to your oven documentation for detailed instructions for doing this. If you are using the GeneChip Hybridization Oven 645, see the GeneChip Hybridization Oven 645 User s Guide, P/N Click the Start button from the Hybridization Oven panel toolbar. If you are using the GeneChip Hybridization Oven 645, AMDS will constantly display the status of the oven in the Device Status panel on the right side of the worklist (Figure 4.20). 7. Once the hybridization is complete, select the specimens that have completed hybridization and click the End button from the Hybridization Oven Worklist toolbar. IMPORTANT: The color of the reported elapsed hybridization time will be yellow if the time is less than the minimum time required by the assay parameters. If the elapsed time falls within the acceptable range (determined by the assay), the color will be green. If the elapsed time is greater than that required by the assay parameters, the color will be red.

82 80 The AMDS User s Guide Rev. B 8. Select Complete Step from the Hybridization Oven Worklist toolbar to advance the test request to the next step in the workflow.

83 chapter 4 Test Request Processing 81 Washing and Staining an Array in the Fluidics Station The following flow chart summarizes the steps required to process a an array from test request creation to the end of the fluidics protocol. The steps in bold are those relevant to the fluidics protocol. This procedure assumes that your workstation is connected to the Affymetrix Fluidics Station 450Dx. Active Worklist Create Add Specimen ID & Assay Name Submit Register Add Array ID Save Complete Step Hybridization Select Tray #; Select Oven # Start End Complete Step Fluidics (add your arrays to modules) Scan Barcode of Array and associated module (or select and fill in Select Module # & Select Station #) Start Complete Step For more detail on the operation of the fluidics station, see the appendix, The Fluidics Station 450Dx, on page 135. Figure 4.21 The Fluidics Worklist button

84 82 The AMDS User s Guide Rev. B Setting Up the Fluidics Station 1. Click the Fluidics button from the workflow (Figure 4.21). The Fluidics Worklist appears. (Figure 4.22). Figure 4.22 The Fluidics Worklist 2. Click the Station Setup button. The Fluidics Station Setup window appears (Figure 4.23). Figure 4.23 The Fluidics Worklist 3. Select the desired assay from the Assay field for each of the fluidics stations.

85 chapter 4 Test Request Processing If the assay module instructions for a particular fluidics station (Station #) require a specific buffer (Wash Buffer A and Wash Buffer B), add the buffers to the fluidics station and enter the wash buffer names or IDs in the Wash Buffer A and Wash Buffer B fields. NOTE: You need to use the module check boxes only if the fluidic station contains faulty modules. 5. Click the Close Setup Screen to return to the Fluidics Worklist. Priming the Fluidics Station If you have not yet primed the fluidics station, see the chapter, Priming the Fluidics Station, on page 157 for details on priming the fluidics station. IMPORTANT: You must prime the fluidics station: when you first start the fluidics station, when you change the wash solutions, before processing a cartridge, if you have performed a shutdown on any module, and if the LCD window instructs you to run a prime protocol. Using the Fluidics Station Once you have set up and primed the fluidics station, you can now proceed to use the fluidics station in your assay. 1. Click the Fluidics button from the Workflow (Figure 4.21). The Fluidics Worklist appears. (Figure 4.22). 2. If you are entering the information manually, select a test request record with the desired array ID and enter the fluidics station number in the Station # field and module number in the Module # field for the test request.

86 84 The AMDS User s Guide Rev. B 3. Insert the arrays into the fluidics station modules. 4. If you are using a barcode reader, scan each array then immediately scan the fluidics station module that will process the array. The array ID on the array will identify the proper test request registered to that array ID. See the section, Using the Barcode Reader, on page 51 for instructions on using the barcode reader. The status of the test request will change to ready. 5. Select the test requests. 6. Click the Start button on the toolbar of the Fluidics Worklist panel. 7. When the status indicates complete, click the Complete Step button to advance the test request to the next workflow step. 8. To shut down the fluidics station, click the Station Setup button. When the Station Setup window appears (Figure 4.23), click the Shutdown Station button.

87 Scanning an Array chapter 4 Test Request Processing 85 The following flow chart summarizes the steps required to process an array from test request creation to the end of the scanning procedure. The steps in bold are relevant to the scanning procedure. This procedure assumes that your workstation is connected to the Affymetrix AutoLoaderDx. Active Worklist Create Add Specimen ID & Assay Name Submit Register Add Array ID Save Complete Step Hybridization Select Tray #; Select Oven # Start End Complete Step Fluidics (Add Arrays to modules) (Scan Barcode of Array and associated module or Select Module # and Select Station #) Start Complete Step Scanner (Add Arrays) Start Complete Step For more details on scanning and running the AutoLoaderDx, see the appendix, The Scanner 3000Dx with AutoLoaderDx, on page 195. Figure 4.24 The Scanner Worklist button

88 86 The AMDS User s Guide Rev. B Scanning the Array in Normal Operational Mode 1. Select Scanner from the Workflow (Figure 4.24). The Scanner Worklist in the center panel will appear (Figure 4.25). Figure 4.25 The Scanner Worklist 2. Load the array cartridges into the AutoLoaderDx. 3. Click the Start button from the toolbar of the Scanner Worklist panel. It is not necessary to select test requests or enter any information or read any barcode. The AutoLoaderDx uses a built-in barcode reader to identify the array ID and thus the test request that you had earlier registered with this array ID. 4. When the scan completes, as indicated by the status for the test request showing complete, click the Complete Step button to advance the test request to the next step in the workflow.

89 chapter 4 Test Request Processing 87 NOTE: For certain assays, as determined by the assay manufacturer, the system may require certain additional information for each test request in order for that test request to run successfully. Failure to enter the additional information prior to completion of the scanning step will cause a failure while attempting to execute the analysis algorithm following the scanning step. The assay manufacturer should provide this information as part of the assay documentation. To enter additional information for a test request: 1. Click on the Specimen ID hyperlink in the Active Worklist for a particular specimen. The Additional Info window will appear (see the section, Adding Additional Information to the Specimen ID, on page 62). 2. Enter requested information then, to save, click the Save and Close button. Scanning Arrays in Manual Mode Manual Scan You can scan one array at a time using the manual scan function. You can use this function to scan arrays that have illegible or missing barcode labels. Do not confuse this with the manual mode that the system administrator can access by clicking the System Management button in the Administrator panel of the worklist. For more detail on this function, see the section, Enable Manual Mode, on page Select Scanner from the Workflow (Figure 4.24). The Scanner Worklist in the center panel will appear (Figure 4.25). 2. Select a test request. The Manual Scan button becomes available. 3. Add some identifying information about the array in the Array ID field. 4. Click the Manual Scan button.

90 88 The AMDS User s Guide Rev. B 5. Open the AutoLoaderDx door. Insert the array into the AutoLoaderDx carousel at Slot #1. Close the door. 6. Click the Start button. The door will lock and the scan will begin. When the scan has completed, the door will unlock. Open the door and remove the array. Stopping a Scan You can stop the AutoLoaderDx in the middle of a scanning run 1. Click the Stop Scan button. The AutoLoaderDx will continue with the current array scan then stop and unlock the door. Adding Arrays During a Scanning Run You can stop the AutoLoaderDx in the middle of a scanning run to add arrays. 1. Click the Add Array button. The AutoLoaderDx will continue with the current array scan then stop and unlock the door. 2. Add your arrays. 3. Click the Start button to resume. NOTE: The AutoLoaderDx will not rescan any previously scanned array.

91 Reviewing Test Results chapter 4 Test Request Processing 89 The following flow chart summarizes the steps necessary to review and process the results of an assay. Active Worklist (in Review Results field) Awaiting Results (view test results window) (add comments required) (complete user name and password) Accept/Reject Figure 4.26 The Review Results Function Reviewing Results Procedure 1. On the Active Worklist and in the Review Results field (Figure 4.26), select the Awaiting Review hyperlink for any of the completed test requests on the Active Worklist to view the Assay Report. The partner designed software will create a particular Results window that is tailored for your particular assay. Each partner created software may display different Results windows.

92 90 The AMDS User s Guide Rev. B In this example (Figure 4.27), a Test Results View window appears. This contains summary information on the assay. In the this example, the information includes but not limited to: - Upload URL the location in the workstation of the uploaded file - Upload Time the time and date of the upload - Specimen ID - Patient Name - Target Preparation Date when a technician prepared the target from the specimen - Test Date when the technician performed the AMDS assay - Array ID the ID of the specific GeneChip array that AMDS used to perform the assay - Uploaded Files the.cel,.dat and audit files that AMDS created from the assay NOTE: This example is only for illustrative purposes. The actual Test Results View will be different for each partner assay. The Additional Info, the Assay Batch and the Assay Home (Assay Landing) windows may also be different. For information on the particular Test Results View for your test result, see the partner assay documentation for your assay.

93 chapter 4 Test Request Processing 91 Figure 4.27 The Test Results View window your particular window will display results different from this 2. Click the View Comments and Errors button to see any added information regarding the assay (Figure 4.28). Figure 4.28 The Audit Log Comments and Errors window

94 92 The AMDS User s Guide Rev. B 3. Click the Close button. 4. In the Test Results View window, Comments field, add any relevant comments regarding this assay. AMDS requires this to complete the review. 5. Fill in your user name and password. 6. Click the Print button if you want to print the report. 7. Click Accept, Reject. (click Close if you would like to exit without completing the review). AMDS will move the completed assay test request to the Non- Active Worklist and archive the assay results in a folder on the workstation. Batch Analysis Assay A special assay type, BatchAnalysisAssay, provides batch analysis functions (Figure 4.29). IMPORTANT: Do not confuse this function with the Assay Batch command to associate reagent lot numbers and test requests. See the section, Associating Reagent Lot Numbers to Multiple Test Requests Assay Batch, on page 70 for information on the Assay Batch command.

95 chapter 4 Test Request Processing 93 Figure 4.29 BatchAnalysisAssay in the Assay Name field See the batch assay manual for details on the specific implementation of the Assay Batch Analysis. For test requests associated with an assay of the Batch Assay Analysis type, you will not be able to assign an array ID in the registration step until you have associated that test request with a batch via the Assay Landing screen. Note that the partner creates the Assay Landing screen. Batch analysis occurs only after AMDS completes the assay run and has created the.cel files for those test requests that you have associated with a particular batch. The.cel files should be ready for analysis at this point at the completion of the run.

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97 Chapter5 THE AMDS ADMINISTRATIVE FEATURES Quick Reference Guide Figure 5.1 and Table 5.1 summarize the functions of the Administrator feature. Figure 5.1 Administrative function buttons Table 5.1 AMDS Quick Reference Guide for administrators If you want to: View your system and audit logs Export your system and audit logs to a CD or DVD Then do this in the Administrator panel: 1. Click the View Logs button. 2. Select your log. 1. Click the View Logs button. 2. Select your log. 3. Click the Export button. 4. Click the Burn button.

98 96 The AMDS User s Guide Rev. B Table 5.1 AMDS Quick Reference Guide for administrators (Continued) If you want to: Install an assay Deactivate an assay Activate an assay Add a user Then do this in the Administrator panel: 1. Click Assay Management 2. Click the Install button. 3. Select the Manifest File for an assay. 4. Select the users to whom you want access to this particular assay. 5. Click the Install button again. 1. Click Assay Management 2. Select the Assay. 3. Click the Deactivate button. 1. Perform the install an assay procedure again on the deactivated assay. 1. Click User Management 2. Click the Add User button. 3. Fill in the user s details User ID, First Name Last Name Comment Password 4. Select the user s role Guest Technician Technologist SystemMaintainer LabSupervisor 5. Select the assay groups associated with this user. 6. Click the Discard Changes or Save Changes button.

99 chapter 5 The AMDS Administrative Features 97 Table 5.1 AMDS Quick Reference Guide for administrators (Continued) If you want to: Edit a user Activate or deactivate a user Change a user s password Then do this in the Administrator panel: 1. Click User Management 2. Select the user. 3. Click the Edit User button. 4. Change the user s details User ID, First Name Last Name Comment Password 5. Change the user s role Guest Technician Technologist SystemMaintainer LabSupervisor 6. Change the assay groups associated with this user. 7. Click the Discard Changes or Save Changes button. 1. Click User Management 2. Click the Edit User button. 3. Check or uncheck Active. 4. Click the Discard Changes or Save Changes button 1. Click User Management 2. Click the Edit User button. 3. Check Change Password Confirm Password 4. Change the password 5. Confirm the changed password 6. Click the Discard Changes or Save Changes button. or, if you want to change your own password: In the User Details panel, click Change Password, change the password, click OK.

100 98 The AMDS User s Guide Rev. B Table 5.1 AMDS Quick Reference Guide for administrators (Continued) If you want to: Change the fluidics station settings Perform a Home, Bleach or Change Tubing procedure Monitor the workstation hard disk volume Then do this in the Administrator panel: Click System Management In-House Service User Performed Service and in the Fluidics Station panel change: 1. the FS450Dx Station (select Select Station) 2. the warning notification to perform a bleach protocol (in the Configuration panel, select and change Bleach Interval Warning Limit). To accept, click the Save button, or if you leave the User Services window and a window appears asking you to accept or reject the changes, click Yes, or if you want to reject the changes, click No or Cancel Note: the warning limit must be less than the alert limit. 3. the alert that is the time interval between performing a bleach protocol has passed (in the Configuration panel, select and change Bleach Interval Alert Limit) 4. the warning notification to change the peristaltic tubing (in the Configuration panel, select and update Change Tubing Warning Limit) Note: the warning limit must be less than the alert limit. 5. the alert notification that the time interval between changing the peristaltic tubing has passed (in the Configuration panel, select and update Change Tubing Alert Limit) Click System Management In-House Service User Performed Service and in the Fluidics Station panel: 1. select Procedure (Beach, Home, Change Tubing) 2. click Perform Click System Management In-House Service User Performed Service and in the System panel view HDD Space Available.

101 chapter 5 The AMDS Administrative Features 99 Table 5.1 AMDS Quick Reference Guide for administrators (Continued) If you want to: View the size of the data file to be exported Change the warning that the workstation hard disk is reaching its space capacity Change the alert that the workstation hard disk has reached its space capacity Perform a self test to determine the health of the system confirm that services are running and check instrument communication View the instrument service logs Archive test request data Then do this in the Administrator panel: Click System Management In-House Service User Performed Service and in the System panel view Export File Size. Click System Management In-House Service User Performed Service and in the System panel, Configuration view, change HDD Space Warning Limit. Note: the warning limit must be greater than the alert limit. Click System Management In-House Service User Performed Service and in the System panel, Configuration view, change HDD Space Alert Limit. Note: the warning limit must be greater than the alert limit. Click System Management In-House Service User Performed Service System Self-Test (in the System panel) Click System Management In-House Service Service Logs Click System Management In-House Service Archive Test Requests select test request record, insert blank CD disc, click Archive

102 100 The AMDS User s Guide Rev. B Table 5.1 AMDS Quick Reference Guide for administrators (Continued) If you want to: Change local time, time zone, day light saving Turn the scanner laser on if the laser was off at system start up Disable the AutoLoader Force the AutoLoader to warm up the array cartridges at positions 1 to 4 in the AutoLoader carousel when starting a scan Approve or reject analysis results, once available, before proceeding Then do this in the Administrator panel: 1. Click System Management In-House Service General Configuration 2. In the Time Zone Editable panel, check Editable Local Time and change the local time 3. In the Time Zone Editable panel, check Time Zone and change the time zone and day light saving status. 4. In the Time Zone Editable panel, check Day Light Saving and select Yes or No. 5. Click the Save button or the Discard Changes button. 1. Click System Management In-House Service General Configuration 2. In the System Configuration Flags panel, check the Turn On Laser box. 3. Click the Save button or the Discard Changes button. 1. Click System Management In-House Service General Configuration 2. In the System Configuration Flags panel, check the Disable AutoLoader box. 3. Click the Save button or the Discard Changes button. 1. Click System Management In-House Service General Configuration 2. In the System Configuration Flags panel, check the Force Array Warm Up box. 3. Click the Save button or the Discard Changes button. 1. Click System Management In-House Service General Configuration 2. In the System Configuration Flags panel, check the Require User Approval box. 3. Click the Save button or the Discard Changes button.

103 chapter 5 The AMDS Administrative Features 101 Table 5.1 AMDS Quick Reference Guide for administrators (Continued) If you want to: Identify the printer (Printer Name) Transfer from online (server network) to offline status. Identify the number of jobs in the queue Purge all the jobs in the queue Resume all printing jobs Backup your firewall settings (not used in IVD systems) Restore your firewall settings (not used in IVD systems) Then do this in the Administrator panel: Click System Management In-House Service User Performed Service Printer Name (view the printer name; you cannot change the printer) Click System Management In-House Service User Performed Service Online/Offline (Select one in the Printer panel) Click System Management In-House Service User Performed Service Number of Jobs in the Queue (View in the Printer panel) Click System Management In-House Service User Performed Service Purge All (in the Printer panel) Click System Management In-House Service User Performed Service Resume All (in the Printer panel) Click System Management In-House Service User Performed Service Last Backup Backup (in the Firewall panel) Click System Management In-House Service User Performed Service Last Backup Restore (in the Firewall panel)

104 102 The AMDS User s Guide Rev. B Viewing Logs The View Logs function allows you to view the system and audit logs for your test requests. View Logs window contains an upper region, or System Log, and lower region, or Audit Log. NOTE: Do not confuse Viewing Logs with the instrument service logs that you can view in System Management In-House Service Service Logs (see the section, Viewing Instrument Service Logs, on page 120). System Logs System logs record various algorithm and computer messages and recorded parameters of the completed assays such as the date/time, the component (i.e., the AMDS Business, Interop, Instrument Control), type (i.e. Error, Info, Comment) or User, etc. NOTE: The system and audit logs may be very big. Take this into consideration before you print. 1. Click the View Logs button. The View Logs window appears (Figure 5.2). The upper region displays the system log information. 2. The current system log is the default window. 3. In the System Log dropdown list, select a system log for a previous period for display. 4. Filter the system log view by date/time, component, type, user, etc. 5. Click the Print button to print the System Log. To export System Log files: 1. Select your file (only one at a time).

105 chapter 5 The AMDS Administrative Features Click the Export button. AMDS formats and stages the selected files for export, and alerts you when the files are ready to burn. 3. Click the Burn button to export the current list to the workstation s CD or DVD. Audit Logs Audit logs various messages and parameters for each of the workflow steps such as the Date/Time, the Workflow Step (i.e. Hybridization, Fluidics, Scan, Report), Type (e.g. Info, Error) or User, etc. 1. Click the View Logs button. The View Logs window appears (Figure 5.2). The lower region displays the audit log. AMDS associates audit logs with a test requests. 2. Click on Browse for Audit Logs button to select a test request for which to view audit log details. 3. Filter the audit log by Date/Time, Workflow Step (i.e. Hybridization, Fluidics, Scan, Report, Type (e.g. Info, Error) or User, etc. 4. Click the Print button to print the Audit Logs. To export Audit Log files: 1. Select your file (only one at a time). 2. Click the Export. AMDS formats and stages the selected files for export, and alerts you when the files are ready to burn. 3. Click the Burn button to export the current list to the workstation s CD or DVD. YouNOTE: You cannot select an additional or external CD or DVD player. AMDS automatically exports the logs to the workstation s single internal player.

106 104 The AMDS User s Guide Rev. B Figure 5.2 The View Logs window: the upper pane contains the System Log; the lower pane contains the Audit Log.

107 chapter 5 The AMDS Administrative Features 105 Managing the Assay The Assay Management function capability to install or deactivate assays. provides the 1. Click the Assay Management button. The Assay Management window appears (Figure 5.3). Figure 5.3 The Assay Management window Installing an Assay In order to install an assay, you must have a valid manifest file. The install assay function allows you to browse to the manifest file and install the assay. The install assay function also requires an LIS Name (LIS Laboratory Information System) and identifies the users who should have access to the assay. 1. Click the Install Assay button. The Assay Installation Dialog appears (Figure 5.4).

108 106 The AMDS User s Guide Rev. B 2. In the Select the Manifest file box, enter or browse to the Manifest file name and directory location. (Note: the assay manufacturer will provide the manifest file). 3. In the LIS name box, enter a unique LIS name for the assay. (This is required even if your current system is not connected to an LIS.) 4. Select the users who should be permitted to run this assay. Click the Select All button to select all the users. Click the Deselect All button to deselect all the users. 5. When the Install button appears, click the Install button. Figure 5.4 The Assay Installation Function Installing a Certificate The AMDS IVD application does not use certificates. The AMDS RUO (Research Use Only) version handles server certificates to enable the AMDS system to trust the RUO Server through https protocols. AMDS assays that perform their analysis on the local workstation do not use certificates. This is known as Local Analysis assays (LA assays).

109 chapter 5 The AMDS Administrative Features 107 AMDS assays that do not perform local analysis and do not return an analysis report require a certificate. This is known as No Analysis assays (NA assays). The setup technician will generate a certificate on the RUO Server at set-up time. Deactivating an Assay The deactivate assay function allows you to deactivate an assay if you no longer use this assay and do not want it to appear as a selection in the AMDS application. 1. Select an assay from the Assay Management panel (Figure 5.3). 2. Click the Deactivate button (Figure 5.5). AMDS moves the target request to the Non-Active Worklist window. NOTE: If you want to activate or re-activate an assay, you must re-install the assay from a separate CD/DVD that contains the assay in question.

110 108 The AMDS User s Guide Rev. B Figure 5.5 The Deactivate Assay function

111 chapter 5 The AMDS Administrative Features 109 Managing the Users The User Management button or to change the characteristics of users. allows you to add 1. Click the User Management button. The User Management window appears(figure 5.6). This screen shows the list of current users and provides buttons for adding or editing users. Figure 5.6 User Management Function Adding a User 1. In the User Management panel toolbar (Figure 5.6), click the Add User button. The Add User window appears (Figure 5.7). 2. Establish the following characteristics of the new user. - Select the Active box to make the user currently active.

112 110 The AMDS User s Guide Rev. B - Deselect the Active box to deactivate a user. - Enter a user ID. - Enter the user s first and last name. - Enter a comment (optional). - Create and confirm a password. - Select the user s role. - Select the type of assay groups to which you want the user to have access. Figure 5.7 The Add User Function 3. Click the Save Changes button. AMDS will commit the information and create the user in the system with the associated roles and permissions. Click the Discard Changes button if you do not want to add the user.

113 chapter 5 The AMDS Administrative Features 111 Editing a User You can change any attribute other than the user name. 1. In the User Management panel toolbar (Figure 5.7), select a user. 2. Click the Edit User button. The Edit User window appears (Figure 5.8). 3. Change to the characteristics of a current user. - Select the Active box to make the user currently active. - Deselect the Active box to deactivate a user. - Enter a user ID - Enter the user s first and last name. - Enter a comment. - Create or change a password. If you want to change a password, select the Change Password box, enter the new password. Enter the password again in the Confirm Password dialog box. - Select the user s role. - Select those assays groups to which you want the user to have access.

114 112 The AMDS User s Guide Rev. B Figure 5.8 The Edit User Function 4. Click the Save Changes button. AMDS will commit the information and change the associated roles and permissions of the user. Click the Discard Changes button if you want to cancel and lose the changes.

115 chapter 5 The AMDS Administrative Features 113 Managing the System System management function enables you to perform various types of simple service on AMDS. When you click on the System Management window, the In-House Services function becomes available. Note that the default window will be the User Performed Service function. The System Management function allows you access to the following functions. User Performed Service This is the default widow of the System Management function. You can view the system s configuration, i.e., the device and instrument settings, and make minor changes to the fluidics station, workstation, scanner, printer and firewall settings. View Service Logs view your device, or instrument, service logs NOTE: Do not confuse the View Service Log function with the View System and Audit logs in the section,viewing Logs, on page 102. Archive Test Requests save test data to a hard drive or CD. General Configuration change the time and time zone settings for your particular location and change the configuration flags for your instruments. Changing the Instrument Settings 1. Click the System Management button. 2. The System Management window appears and displays the In- House Service dropdown list (Figure 5.9). If you are not already on the default User Performed Service window, select In-House Service User Performed Service.

116 114 The AMDS User s Guide Rev. B Managing the Fluidics Station The appendix, The Fluidics Station 450Dx, on page 135 provides greater detail on using and maintaining the fluidics station. 1. Click the System Management button. 2. The System Management window appears and displays the In- House Service dropdown list (Figure 5.9). Figure 5.9 The In-House Services function If you are not already in the default User Performed Service window (Figure 5.10), select In-House Service User Performed Service. View the Fluidics Station panel (Figure 5.10). Figure 5.10 The management functions for the fluidics station 3. Select a station number from the drop down list. The system will show the last bleach and peristaltic tube change. 4. If you want to perform a bleach protocol, select Bleach in the Procedure dialog box and see the section, The Bleach Cycle, on page 161 for details on using the bleach protocol.

117 chapter 5 The AMDS Administrative Features If you want to change the tubing, select Change Tubing in the Procedure dialog box and see the section, Peristaltic Tubing Maintenance, on page 169 for more details on changing the peristaltic tubes. 6. If you are having problems communicating with the fluidics station or just want to test the communications, select Home in the Procedure dialog box and click the Perform button. The Confirm Step dialog box appears. Enter your password and the Event Reason. Click OK. AMDS will instruct the fluidics station to home the valves. If successful, the LCD on the fluidics station will inform you. If homing fails, the Device Status panel on a worklist window will alert you. If you fail after several unsuccessful tries to home the fluidics station, turn off then turn on the fluidics station. If these failures continue, call Affymetrix technical support. 7. In the Configuration panel, set the Bleach Interval Warning Limit, Bleach Interval Alert Limit. 8. Click the Save button. 9. The Confirm Step dialog box appears. Enter your password and the Event Reason. Click OK. 10.In the Configuration panel, set the Change Tubing Warning Limit and Change Tubing Alert Limit. NOTE: The warning limit times must be less than the alert limit times. 11.Click the Save button. 12.The Confirm Step dialog box appears. Enter your password and the Event Reason. Click the OK button.

118 116 The AMDS User s Guide Rev. B Managing the Workstation You can monitor the amount of space on the workstation s hard disk and the size of the data file size that you export. 1. Click the System Management button. 2. The System Management window appears and displays the In- House Service dropdown list (Figure 5.11). Figure 5.11 The In-House Services function If you are not already on the default User Performed Service window, select In-House Service User Performed Service. View the System panel (Figure 5.12). Figure 5.12 The management functions for the workstation 3. To view the hard drive space available and the size of the data file for saving to the hard drive click the System Self-Test button to perform a system self test. 4. To restart the AutoLoaderDx, click the Restart Scanner button. Use this function if you are experiencing problems connecting to the AutoLoaderDx. Clicking this button will attempt to restart AutoLoaderDx and establish communication between the workstation and the AutoLoaderDx. 5. To view and manage the Intel RAID Matrix volumes and to check the health of your hard drives, click the RAID Storage Console button.

119 chapter 5 The AMDS Administrative Features 117 The Intel Matrix Storage Console window appears and displays information on your hard drives (Figure 5.13). Figure 5.13 The RAID Matrix Storage Console window 6. To set a warning and alert that informs you that you are reaching the capacity limit of your hard disc drive, in the Configuration panel, set the HDD Space Warning Limit, HDD Space Alert Limit. Click the Save button. NOTE: The warning limit times must be less than the alert limit times. Managing the Printer You can perform several printer maintenance functions. You can: Transfer from online to offline status. Identify the number of jobs in the queue

120 118 The AMDS User s Guide Rev. B Purge all the jobs in the queue Resume printing 1. Click the System Management button. 2. The System Management window appears and displays the In- House Service dropdown list (Figure 5.14). Figure 5.14 The In-House Services function If you are not already on the default User Performed Service window, select In-House Service User Performed Service. View the Printer panel (Figure 5.15). NOTE: You cannot change the printer. The Affymetrix service technician set up the printer when he installed the AMDS system. Figure 5.15 The management functions for the printer 3. View the printer name. 4. To send the printer offline (for printer maintenance, etc.) and stop the printing of the job queue, select Offline. 5. To bring the printer online, select Online. The Print button in the workflows will become enabled.

121 chapter 5 The AMDS Administrative Features Click the Purge All button to cancel all the jobs in the print queue. 7. To print all the jobs in the queue, click the Resume All button to continue printing the job queue. Managing the Firewall Settings The AMDS firewall monitors incoming and outgoing messages from the workstation and protects the workstation from malicious intrusion (Figure 5.16). Users can backup and restore firewall settings. Figure 5.16 The user maintenance functions for the printer

122 120 The AMDS User s Guide Rev. B Viewing Instrument Service Logs You can open and view the service logs for the instruments. 1. Click the System Management button. 2. Select In-House Service Service Log (Figure 5.17). Figure 5.17 The In-House Service tab The User Performed Service Log screen will appear in the center panel. You can filter the log by Date/Time, Procedure, User or Device (Figure 5.18). Figure 5.18 The User Performed Service Logs window

123 chapter 5 The AMDS Administrative Features 121 Archiving Test Requests 1. Click on the System Management button. 2. Select In-House Service Archive Test Requests (Figure 5.19). Figure 5.19 The In-House Service tab The System Management Archiving screen will appear in the center panel (Figure 5.20). Figure 5.20 The System Management Archiving window 1. Filter the log by Date Completed, Assay Name, Assay Version, or Array ID. 2. Select those test requests you wish to archive. 3. Click the Archive button to archive the test request records

124 122 The AMDS User s Guide Rev. B 4. After you have archived the test request records, you can click the Purge button if you want to delete the archived test request records from the system. IMPORTANT: You can only purge a test request record after you have archived it. Once you purge a test request record, you cannot recover it. Setting the General Configuration In the General Configuration window you can view and set the time zone and set several system configuration flags. 1. Click on the System Management button. 2. Select In-House Service General Configuration (Figure 5.21). Figure 5.21 The In-House Service tab The General Configuration window appears (Figure 5.22).

125 chapter 5 The AMDS Administrative Features 123 Figure 5.22 The General Configuration window Setting and Viewing Date and Time You can set the local time, time zone, and savings time. In the Time Zone Editable Settings panel: 1. In Editable Local time, set the local time. 2. In Time Zone, set your local time zone. 3. In Daylight Savings, select Yes or No. In the Time Zone Current Settings panel, view the local time, time zone, and savings time.

126 124 The AMDS User s Guide Rev. B Managing the AutoLoaderDx In the System Configuration Flags window, you can control three functions of the AutoLoaderDx and require user approval (Figure 5.23). You can control the following three functions of the AutoLoaderDx: Turn on scanner every time you launch AMDS. Disable the AutoLoaderDx to run only the software. Force arrays 1 to 4 to warm up when you start scanning a run to speed up the run. This is faster than warming each array one at a time. Figure 5.23 The System Configuration Flags window In the System Configuration Flags window: 1. Select Turn on Laser to turn on the AutoLoaderDx laser automatically when you launch the AMDS application. 2. Select Disable AutoLoader box to disable the AutoLoaderDx and use just the AMDS application without the AutoLoaderDx. 3. Select Force Array Warm Up if the arrays are not already at room temperature, and you want raise the temperature of the arrays in carousel positions 1 to 4 before scanning.

127 chapter 5 The AMDS Administrative Features 125 Requiring User Approval for the Analysis Results Select Require User Approval to require the technician to approve or reject the analysis results as they become available after an assay run (Figure 5.23). This flag is meaningful only if your AMDS system is connected to a laboratory information system (LIS) network. Selecting this box when you are connected to a LIS allows you to make a final determination as to whether or not the test request assay run is complete before the software uploads the test request results to the LIS. NOTE: If you are not connected to a LIS, you must select this box so that the technician will have a method of approving or rejecting the results.

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129 Chapter6 AMDS TROUBLESHOOTING Introduction There are generally three categories of problems that can cause trouble when executing test requests: Instrument related problems, such as problems with the Hybridization Oven, problems with a fluidics station or module, or problems with the scanner. Problems with a particular test request, for example the bar code of the array associated with a test request could not be read, or gridding fails for a test request. Operational errors, including data input errors. The system tracks and reports on all three categories of problems mentioned above. This section provides information as to how to identify that a problem has occurred, and provides some general guidance as to how to try to resolve a problem.

130 128 The AMDS User s Guide Rev. B First Type of Problem Resolving Instrument Related Errors The status of the various instruments are displayed in the Device Status panel (Figure 6.1). Figure 6.1 The Device Status Panel Generally if an instrument, such as the Hybridization Oven 645, fluidics station or scanner functions properly, the Status column displays a Green icon next to the instrument name. This is the first place to look if you suspect trouble with an instrument. If a problem arises in an instrument, AMDS will raise an alert. Alerts inform you of the problem that occurred and provides suggestions as to how to resolve the alert.

131 chapter 6 AMDS Troubleshooting 129 If the device status screen indicates a problem with an instrument, examine the alerts list for additional detail (Figure 6.2). To address the problem, open the alert to receive additional information on the alert, and follow the suggested resolution to resolve the problem. Once resolved, clear the alert by following the Resolving Alerts procedure below. In many cases, you may not be able to resolve an instrument problem. In these cases, call an Affymetrix service technician to resolve the problem. You should not attempt to correct this kind of problem yourself. Second Type of Problem Resolving Individual Test Requests Errors The second category of troubleshooting relates to problems with an individual test request. You can resolve several errors that can occur relating to a test request, these include: Scanner could not read the bar code. Autofocus error. Gridding error. Analysis algorithm error as a result of missing information. As with the instrument errors, the test requests errors will raise an alert. Refer to the individual alert for additional information and a suggested course of action for resolving the error. Once you have resolved the error, AMDS can proceed with the assay run. Third Type of Problem Resolving Operational and Data Input Errors The third and final category of error consists of operational or data input errors. These type of errors are relatively easy to detect and correct as the User Interface is designed to provide immediate feedback and prevent incorrect operation and/or data input. Some examples of incorrect operation or data input include: Entry of an invalid Array Barcode. Selection of an assay type that has not been installed on the system.

132 130 The AMDS User s Guide Rev. B Batching of arrays that require different hybridization temperatures. Loading of an array into a fluidics station that is not primed. Loading of an array into a fluidics station that is configured for a different assay type. Starting a workflow step on an array before it has completed the required prerequisite workflow steps, for example, scanning an array while AMDS is still processing that array s test request in the fluidics worklist. In each of these cases, AMDS will immediately display an error message that informs you the action or data entered is inappropriate and prevents you from proceeding. Resolving Alerts During the processing of test requests through the workflow, any issues encountered by the system will be communicated to the user through the Alerts panel. You can clear these alerts (Figure 6.2).

133 chapter 6 AMDS Troubleshooting 131 Figure 6.2 User Alert Function Resolving Alerts Procedure 1. From any workflow window, double-click on an alert in the Alerts panel. The Alert Details panel will appear in the lowerright corner of the screen (Figure 6.3).

134 132 The AMDS User s Guide Rev. B Figure 6.3 User Alert Function 2. If the Alert has a Specimen ID associated with it, use the Go To test request button to select the row in the current worklist that contains the related test request. 3. After resolving the issue, click the Resolve button and enter an e-signature to continue processing the test request. Instrument Troubleshooting Many instrument errors will require the attention of a qualified Affymetrix field service engineer. However, there are some errors that can be resolved and are listed here.

135 chapter 6 AMDS Troubleshooting 133 Fluidics Station The station is not primed: You can access the fluidics setup window to prime the fluidics station for the selected assay class. See the section, Priming the Fluidics Station, on page 157. Fluidics station configured for a different assay: Open the fluidics station set up window to reconfigure the station for the correct assay type. You can also use a fluidics station that already has the correct assay type selected. See the section, Setting Up the Fluidics Station, on page 82 for details on changing the assay type. Missing fluid error: You can supply the necessary fluid, clear the alert and resume the fluidics run. You can change the fluids and prime the fluidics station. If you continue to see this error, it may indicate a system failure. Call Affymetrix technical support. See the section, Fluidics Station Troubleshooting and Assistance, on page 173. AutoLoader Autofocus error: This error generally occurs if the probe cartridge glass substrate is smudged or dirty, usually with a thumb print. Clean the array, clear the alert and retry. Barcode could not be read: Retrieve the array and process using the manual scan procedure. See the section, Scanning Arrays in Manual Mode Manual Scan, on page 87. For more information on AutoLoaderDx troubleshooting, see the section, Troubleshooting, on page 214.

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137 Appendix A THE FLUIDICS STATION 450DX Introduction This chapter introduces the Affymetrix GeneChip Fluidics Station 450Dx (aka the fluidics station) and its components, gives an overview of how the fluidics station works, and covers the safe use of the fluidics station. The fluidics station is part of the AMDS that includes the GeneChip AutoLoaderDx.

138 136 The AMDS User s Guide Rev. B Warnings and Precautions Installation and de-installation of the system must be done by a trained Affymetrix representative. The system warranty may be voided if used in a manner not specified by the manufacturer. Exercise the normal precautions that are required for handling all laboratory reagents. Wear gloves when using the fluidics station. Exercise standard precautions when obtaining, handling, and disposing of potentially carcinogenic reagents. Do not send your instrument elsewhere for service or attempt to service it yourself. To protect your warranty and ensure safe operation, the instrument should be serviced only by Affymetrix or its representatives. If the instrument is not working correctly, please contact your Affymetrix Technical Support representative. Do not use the fluidics station in ways not specified by Affymetrix. Doing so may impair the protections provided by the fluidics station. WARNING: Do not place hands or fingers inside the cartridge holder. Under electrical load conditions, the area behind the cartridge holder can have temperatures that rise to 100 C or higher. The fluidics station requires two people to lift and handle it safely. Each person should firmly grasp the base of the instrument at the end opposite the other to lift. Use OSHA standards for lifting techniques. The instrument must be surrounded by adequate airspace. Slots and openings in the instrument and the electronics compartment covers are for ventilation. Do not block or cover them. Never push an object into the instrument ventilation slots; equipment damage or injury may result. Do not set liquids on top of the instrument. The FS450Dx is intended for indoor, laboratory use in a controlled environment.

139 appendix A The Fluidics Station 450Dx 137 Caution Notices: CAUTION You must have read and understood the contents of this manual before attempting to operate this fluidics station. CAUTION The power supply cord is used as the main disconnect device. Ensure that the socket outlet is located and installed near the equipment and is easily accessible.

140 138 The AMDS User s Guide Rev. B Instrument Components The GeneChip Fluidics Station 450Dx (aka the fluidics station) contains four modules. Each module can hold one GeneChip array cartridge and up to three vials. The software and computer workstation can control each of the four modules independently of the others. You can use any or all of the modules at the same time. The modules are numbered 1 through 4 near the LCD window. Figure A.1 and Figure A.2 show the components and cable connections of the fluidics station. See Figure B.2 on page 201 for the cable connection to the AutoLoaderDx. This is for reference only. Affymetrix recommends that only a qualified service technician attempt to service this instrument or change these connections. The GeneChip Fluidics Station 450Dx includes the following components. 1. Sample Holders holds up to three sample vials 2. Module Door protective cover for the peristaltic pump on the module 3. Cartridge Holder holds the cartridge during fluidics operation 4. Washblock part of the cartridge holder that completes the fluid path when a cartridge is not in place (used for cleaning out or draining the fluidics station) 5. Cartridge Lever engages or releases the cartridge holder 6. Needle Lever inserts the needles into the sample vials 7. LCD Window displays messages during processes 8. Lid Release Buttons one on each side (on older fluidics station models. New models open merely by lifting the lid.) 9. Wash Bottles (2) hold wash buffers and tubing that draws buffer through system 10. DI Water Bottle holds deionized water and tubing that draws water through system 11. Waste Bottle collects waste from hybridizations and washes

141 appendix A The Fluidics Station 450Dx Sample or Vial Needles extend into the sample vials and draw fluid. 13. Barcode Label each module has an associated barcode to identify the module that is used by the worklist. 6. Needle Lever 3 & 4. Wash block and Cartridge Holder 13. Barcode Label 7. LCD Window 8. Lid Release Button (on older fluidics station models) 9. Wash B Bottle 9. Wash A Bottle 2. Module Door 10. DI Water Bottle 5. Cartridge Lever 11. Waste Bottle 12. Sample Needles (extended) 1. Sample Holder Figure A.1 The GeneChip Fluidics Station 450Dx and components

142 140 The AMDS User s Guide Rev. B CommLink Out Connector (to terminator or cable to next fluidics station) CommLink In Connector Power Cable ON/OFF Switch (Power Main) Lid Release Button (Note: these buttons may be present or absent depending on the model of the fluidics station.) Figure A.2 Location of the serial ports and ON/OFF switch

143 Using the Fluidics Station 450Dx appendix A The Fluidics Station 450Dx 141 This section shows you how to run the fluidics station. Assay Documentation You must configure the fluidics station for the type of assay that you will run on the fluidics station. The partner who provides the assay will determine the assay type and will provide the relevant documentation in the form of a package insert or other type of document. Each assay package insert, or assay document, will describe the fluidics station configuration requirements for that assay. The system will ensure that the fluidics station is configured properly for the assay being run. If the station is not configured properly for the assay, you will be notified. You may then configure the station for that assay, or run the test request on a fluidics station that is correctly configured for that assay.

144 142 The AMDS User s Guide Rev. B Using the Barcode Reader with the Fluidics Station 1. Open the Fluidics Worklist. 2. Hold the array or insert the array into the fluidics station module. 3. Aim the barcode reader at the barcode of the array and record the barcode number. 4. Aim the barcode reader at the barcode of the fluidics module and record the barcode number. The AMDS software will locate the appropriate fields in the Fluidics Worklist and add the numbers. The barcode reader emits three distinct sounds depending on the sound s function. a. A good sound that indicates that the barcode reader recorded the correct test request b. A double good sound that indicates that the barcode reader confirms a valid association c. A bad sound that indicates that the barcode reader detects an error. Check the relevant AMDS window for information on the error. See the section, Using the Barcode Reader, on page 51 for more information on using the barcode reader. See the section, Connecting the Barcode Reader, on page 203 for information on connecting the barcode reader to the workstation. The Fluidics Station 450Dx Protocols This section describes in summary detail how to use the Fluidics Station 450Dx with sample protocols. See the section, Washing and Staining an Array in the Fluidics Station, on page 81 for details on using the fluidics station to process arrays.

145 appendix A The Fluidics Station 450Dx 143 NOTE: These instructions are for use with the AMDS software. Please consult partner assay instructions for use as needed. For more specific information on hybridizing the target to the array cartridge, refer to the appropriate package insert. Setting Up an Assay Before running a protocol on the fluidics station, you must first define an assay in the AMDS software. For information on defining an assay, refer to the assay instructions or to the appropriate package insert. See also the chapter, Creating, Editing and Cancelling Test Requests The Active Worklist, on page 60. Sample Hybridization Protocol Using the Fluidics Station If you are to hybridize an array on the fluidics station, the following steps briefly illustrate the protocol. 1. Start from the fluidics worklist and use the applicable assay product insert or partner s documentation to start the fluidics station protocol. 2. Place a new assay-specific array cartridge containing the specimen sample into the cartridge holder on the selected module of the fluidics station. Gently pull up on the cartridge lever to close the washblock and engage the array. 3. Depending on the assay instructions, place appropriately prepared sample vials in the sample vial holders as indicated on the fluidics station LCD. Please note that the indicated position may be different depending on the particular assay protocol used. 4. The fluidics station will perform the following actions to hybridize the bound target to the probe on the cartridge and prepare it for washing. The fluidics station will:

146 144 The AMDS User s Guide Rev. B - draw hybridization cocktail from the vial into the cartridge and mix it by alternately draining and filling the cartridge at a selected temperature for the time set by the assay manufacturer; - expel the hybridization cocktail back into the sample tube, or into the waste line, at the end of the hybridization step, depending on the assay manufacturer's specifications; - clean the module tubing and needles for the next cartridge to be processed. Sample Staining Protocol If you will be staining an array, the following steps illustrate the protocol. 1. Start from the fluidics worklist and use the applicable assay product insert or partner s documentation to start the fluidics station protocol. 2. After the hybridization of the array, the array remains in the cartridge holder. If you have removed the array for any reason, replace the same array cartridge into the cartridge holder on the selected module of the fluidics station. Gently flip the cartridge lever to close the washblock and engage the array. 3. Depending on the assay instructions, place appropriately prepared vials in the sample vial holders as indicated on the fluidics station LCD. Please note that the indicated position may be different depending on the particular assay protocol used. 4. The fluidics station will perform the following actions to stain the bound target on the cartridge and prepare it for scanning. The fluidics station will: - wash the cartridge with wash solution (or solutions) at a selected temperature; - draw staining solution from the vial into the cartridge and mix it by alternately draining and filling the cartridge at a selected temperature; - expel the staining solution to the waste line;

147 appendix A The Fluidics Station 450Dx fill the cartridge with wash solution for scanning; - clean the module tubing and needles for the next cartridge to be processed. - After staining and washing, the AutoLoaderDx scans the cartridge by laser light to obtain fluorescence intensity data. For information on using the scanner, see the section, Scanning an Array, on page 85. Operating the Fluidics Station This section illustrates how to operate the fluidics station to process assays. This discussion must be general since the number and type of steps required to process your specific array will be different depending on the specific design of the assay that the array contains. IMPORTANT: Do not lower needles or engage the washblock until prompted by the fluidics station LCD. Starting the Fluidics Station 1. Check to ensure that the fluidics station is connected to the power main through the power cord provided. 2. Check to ensure that the fluidics station is connected to the workstation. CommLink connections are located on the back of the fluidics station. See Figure A.2 on page Flip the ON/OFF switch for the fluidics station to the ON position. The switch is located on the left side of the fluidics station. See Figure A.2 on page 140. The LCD window should display the following: Power-On Done NOT PRIMED 25 C

148 146 The AMDS User s Guide Rev. B 4. If you have not done so already, turn on the computer workstation. The AMDS software will automatically open. Running a Fluidics Station Protocol The following steps represent a general procedure. Your specific protocol may indicate steps different from these outlined below. 1. Check to ensure that all the wash lines are in the appropriate wash bottles. Please consult the array package insert that came with the cartridge kit for the appropriate wash buffer solutions, or contact your Affymetrix technical support representative. 2. If you have not yet primed the fluidics station for the new assay, prime the fluidics station now. See the section, Priming the Fluidics Station, on page Load three standard 1.5 ml vials in the sample holders of each module that is to be primed (Figure A.7). 4. In the Active Worklist main window (Figure A.3). Click the Fluidics icon button. The Fluidics Worklist appears (Figure A.4). Figure A.3 Click the Fluidics icon to gain access to the fluidics control screen

149 appendix A The Fluidics Station 450Dx 147 Figure A.4 The Fluidics Worklist 5. If you are manually associating a test request with a fluidics station and module do the following: a. In the test request record that contains the desired Specimen ID, place the cursor in the Station # field and enter the station number. b. Place the cursor in the Module # field and enter the module number. c. Place the array cartridge in the module washblock (Figure A.5). Do not engage the washblock until prompted by the fluidics station LCD. The module must be the same as the module that you earlier associated with the array(figure A.5).

150 148 The AMDS User s Guide Rev. B Figure A.5 Inserting the cartridge into the cartridge holder - note orientation and array label 6. If you using a barcode reader to associate a test request with a fluidics station and module do the following (See the section, Using the Barcode Reader, on page 51):

151 appendix A The Fluidics Station 450Dx 149 a. Load the array cartridge into the module washblock (Figure A.5). The module must be the same as the module that you earlier associated with the array. b. Scan the barcode on the array cartridge. c. Scan the barcode on the fluidics station module. 7. Select the test request rows that indicate Ready in the Status field. 8. Click the Start button to begin the fluidics protocol. The LCD window on the fluidics station and the AMDS Status field in the Fluidics Worklist window will indicate the status of the protocol as it progresses. 9. Follow the instructions on the fluidics station LCD window or in the AMDS fluidics station field (see also the section, FS450Dx LCD Messages, on page 184 for more LCD messages). A selection of the available prompts is given below as examples: - If prompted to: LOAD VIALS load the 1.5 ml vials into the sample holder of the fluidics station. - If prompted to: LOAD CARTRIDGE Since you earlier loaded an array cartridge into the fluidics station module, you must now engage the washblock. Flip the cartridge lever up to engage the cartridge septa needles into the septa. Proper engagement of the washblock with the cartridge is indicated by a change in the message on the LCD (Figure A.6).

152 150 The AMDS User s Guide Rev. B Figure A.6 Flip the cartridge lever up to engage the cartridge septa needles into the septa.

153 appendix A The Fluidics Station 450Dx 151 IMPORTANT: To minimize damage to the array, the door closure forces are controlled. If you cannot get proper engagement, simply press on the washblock to complete the action. Do not force anything. Press on the washblock. DO NOT FORCE UP THE CARTRIDGE LEVER. 10. If prompted to: LOAD VIALS 1-2-3

154 152 The AMDS User s Guide Rev. B place the three 1.5 ml sample vials containing reagents into the sample holders 1, 2 and 3 on the fluidics station in accordance with the assay instructions (Figure A.7). Needle Lever in Up Position Vials Figure A.7 The sample vials on the sample holder with the needle lever up note the orientation of the vial caps. NOTE: When you place the vials into the holders, orient the vial caps toward you so that the vials seat snugly into their respective holders. d. When you have loaded the vials, gently but firmly press down on the needle lever to insert the needles into the vials. The run will commence automatically. See Figure A.8 and Figure A.9.

155 appendix A The Fluidics Station 450Dx 153 Figure A.8 Press down on the needle levers to start the protocol.

156 154 The AMDS User s Guide Rev. B Figure A.9 The sample vials on the sample holder with the needle lever down note the orientation of the vial caps. As the run progresses, check to ensure that the cartridge is filling properly and that bubbles are not forming. If it is not filling properly, see the note below in this chapter. 11. When you have completed the hybridization, or washing and staining protocols, the LCD window should display the following: EJECT CARTRIDGE

157 appendix A The Fluidics Station 450Dx Eject and remove the cartridge by pushing down on the cartridge lever. The LCD window should display the following: ENGAGE WASHBLOCK NOTE: If air bubbles are present in the cartridge, return it to the cartridge holder. Engage the washblock by pulling up on the cartridge lever to the closed position. The fluidics station will drain the cartridge and then fill it with a fresh volume of the last wash buffer used. When it is finished, if the LCD window displays EJECT CARTRIDGE again, remove the cartridge and inspect it again for bubbles. If no bubbles are present, it is ready to scan; proceed to step Flip up the cartridge holder lever to re-engage the wash block. 14. Lift up on the needle lever to remove the needles from the vials. 15. Replace the used vials with new empty vials. 16. Press down on the needle lever. The fluidics station will automatically perform a Cleanout protocol. The LCD window will indicate the progress of the Cleanout protocol. When the Cleanout protocol is complete, the LCD window should display the following: REMOVE VIALS 17. Lift the needle lever and remove the sample vials from the sample holder.

158 156 The AMDS User s Guide Rev. B Shutting Down You should perform the Shutdown protocol at the end of a session. Do not keep the fluidics station on if you will not use it again within the next 12 hours. This will reduce the risk of salt buildup in the instrument. 1. As with the prime protocol, the shutdown protocol requires three 1.5 ml sample vials for each module. 2. After removing an array from the array holder, the LCD window displays the message: ENGAGE WASHBLOCK 3. Engage the washblock by gently flipping up on the array cartridge lever to the up position. 4. Press down on the needle lever. The fluidics station automatically performs a Cleanout protocol. The LCD window indicates the progress of the Cleanout protocol. 5. When the fluidics station LCD window indicates: REMOVE VIALS the fluidics station has completed the Cleanout protocol. 6. Remove the sample vials from the sample holder. 7. If no other hybridizations are to be performed, place the wash lines into a bottle filled with deionized water. 8. Run the Shutdown protocol. 9. After the Shutdown protocol is complete, flip the ON/OFF switch to the OFF position.

159 appendix A The Fluidics Station 450Dx 157 IMPORTANT: To maintain the cleanliness of the fluidics station and obtain the highest quality image and data possible, a weekly bleach protocol. Please refer to the section, Fluidics Station Bleach Protocol, on page 160 for further details. Priming the Fluidics Station Priming fills the fluidics station lines with wash buffers designed for that assay and deionized water. You must prime the Fluidics Station FS450Dx before you can use it to run assay protocols. You should prime the fluidics station: when you first start the fluidics station, when you change the wash solutions, before processing a cartridge if you have performed a shutdown on any module, and if the LCD window instructs you to run a prime protocol. 1. Check to ensure that all the wash lines are in the appropriate wash bottles. Please consult the array package insert that came with the cartridge kit for the appropriate wash buffer solutions, or contact your Affymetrix technical support representative. 2. Load three standard 1.5 ml vials in the sample holders of each module that is to be primed (Figure A.7). 3. In the Active Worklist main window (Figure A.10). Click the Fluidics icon button. The Fluidics Worklist appears (Figure A.11).

160 158 The AMDS User s Guide Rev. B Figure A.10 Click the Fluidics icon to gain access to the fluidics control screen Figure A.11 The Fluidics Worklist

161 appendix A The Fluidics Station 450Dx Click the Station Setup button. 5. The Fluidics Station Setup widow appears (Figure A.12). 6. In the Fluidics Station Setup window, select the Station #, the Assay and the Modules to be primed. 7. Click the Prime Station button. Figure A.12 The Fluidics Station setup window The status field will display the priming message (Figure A.13). Figure A.13 The Priming Status field 8. Follow the instructions in the LCD window on the fluidics station as the prime protocol progresses. The LCD window on the fluidics station and the fluidics station dialog box will indicate the status of the prime and when AMDS has completed the priming protocol. After you have primed the fluidics station, you are ready to hybridize or wash and stain a sample.

162 160 The AMDS User s Guide Rev. B Fluidics StationDx Care and Maintenance Introduction This chapter provides instructions on caring for and maintaining the instrument, and on troubleshooting if problems arise. Instrument Care Use a surge protector on the power line to the fluidics station. Always run a Shutdown protocol when the instrument will be off or unused overnight or longer. This will prevent salt crystals from forming within the fluidics system. When not using the instrument, leave the sample needles in the lowered position. Each needle should extend into an empty vial. This will protect them from accidental damage. Always use deionized water to prevent contamination of the lines. Change buffers with freshly prepared buffer at each system startup. The fluidics station should be positioned on a sturdy, level bench away from extremes in temperature and away from moving air. Fluidics Station Bleach Protocol This protocol is designed to eliminate any residual SAPE-antibody complex that may be present in the fluidics station tubing and needles. The protocol runs a bleach solution through the system followed by a rinse cycle with deionized (DI) water. This protocol takes approximately one hour and forty minutes to complete. Affymetrix recommends running this protocol weekly. If you have AMDS administrator privileges, you can set the Bleach Interval Warning Limit and Bleach Interval Alert Limit. See the section, Managing the Fluidics Station, on page 114. To avoid carryover, or cross contamination, from the bleach protocol, Affymetrix recommends the use of dedicated bottles for bleach and DI water. You can obtain additional bottles from Affymetrix.

163 B appendix A The Fluidics Station 450Dx 161 Part Number Description Media Bottle, SQ, 500mL Media Bottle, SQ, 1000mL The Bleach Cycle 1. Disengage the washblock for each module by pressing down on the cartridge lever. Remove any array cartridge (Figure A.14). AFFYMETRIX P/N Remove cartridges (if any) DXM0776 Washblocks disengaged with cartridge Figure A.14 Disengaged washblocks showing cartridge levers in the down position; remove any cartridges

164 162 The AMDS User s Guide Rev. B 2. Prepare 500 ml of 0.525% sodium hypochlorite solution using deionized water. Shake well. For example: follow these directions to make 500 ml of bleach. In a 1 liter plastic or glass graduated cylinder combine ml of commercial bleach (such as Clorox bleach 1, which is 6% sodium hypochlorite) with ml of DI H 2 O, mix well. Pour the solution into a 500 ml plastic bottle, and place the plastic bottle on the fluidics station. IMPORTANT: The shelf life of this solution is 24 hours. After this period, you must prepare a fresh solution. NOTE: Each fluidics station with four modules requires 500 ml of the 0.525% sodium hypochlorite solution. 3. Place on the fluidics station an empty one liter waste bottle, a 500 ml bottle of bleach and a one liter bottle of DI water. Insert the waste line into the waste bottle (Figure A.15). 4. Immerse all three wash and water lines of the fluidics station into the 500 ml of bleach solution (Figure A.15). DO NOT IMMERSE THE WASTE LINE INTO THE BLEACH. IMPORTANT: The bleach protocol requires approximately one liter of deionized water. 1 Affymetrix also recommends the new Clorox Ultra Bleach (with 6.15% sodium hypochlorite) but your mixing calculations will be different.

165 appendix A The Fluidics Station 450Dx 163 Figure A.15 Immerse the tubes into the 0.525% sodium hypochlorite solution. The waste line remains in the waste bottle. 5. In the AMDS software, click the System Management button the menu (Figure A.16).

166 164 The AMDS User s Guide Rev. B Figure A.16 Click the System Management button to gain access to maintenance functions. 6. The System Management window appears. The User Performed Service window should be the default window. If not, select In-House Service User Service. The User Performed Service window appears. Note the fluidics station maintenance area (Figure A.17). Figure A.17 The user maintenance functions for the fluidics station 7. From the dropdown list, select a station number. The system will show the last bleach and peristaltic tube change. 8. Select the Bleach procedure from the dropdown list and click the Perform button. The Confirm Step dialog box opens. Enter your password and event reason. AMDS enters the time and date information into the device log.

167 appendix A The Fluidics Station 450Dx 165 CAUTION: Temperature will ramp up to 50 C. i 9. Follow the prompts on the LCD. Load three empty 1.5 ml vials onto each module if you have not already done so. 10. Press down on each of the needle levers to start the bleach protocol (Figure A.8). Figure A.18 Press down on the needle levers to start the bleach protocol.

168 166 The AMDS User s Guide Rev. B 11. The fluidics station will begin the protocol and begin to empty the lines and perform the cleaning cycles using bleach solution. 12. After approximately 30 minutes, the LCD will prompt you when the bleach cycle is over and the rinse cycle about to begin. The Rinse Cycle Once the bleach cycle has finished, the second part of the protocol is a rinse step. This step is essential to remove all traces of bleach from the system. Failure to complete this step can result in damaged arrays. 1. Follow the prompts on the LCD for each module. Lift up on the needle levers and remove the bleach vials. Load clean, empty vials onto each module. 2. Remove the three wash and water lines from the bleach bottle and transfer them to the DI water bottle (Figure A.19). At this step, you need not be concerned regarding the bleach that remains in the lines.

169 appendix A The Fluidics Station 450Dx 167 Figure A.19 Immerse the three wash and water lines in the DI water bottle. The waste line remains in the waste bottle. 3. Press down on the needle levers to begin the rinse cycle. The fluidics station will empty the lines and rinse the needles. 4. When the rinse is completed after approximately one hour, the fluidics station will bring the temperature back to 25 C and drain the lines with air. The LCD display will read: CLEANING DONE 5. Discard the vials employed for the bleach protocol.

170 168 The AMDS User s Guide Rev. B 6. Follow these suggestions in Table A.1 after you have completed the bleach protocol. Table A.1 Suggestions on using the FS450Dx after a bleach protocol If you are: Planning to use the system immediately Not planning to use the system immediately Not planning to use the system for an extended period of time (longer than one week) Then do this: After running the bleach protocol, remove the DI water supply used in the rinse phase and install the appropriate reagents for use in your next staining and washing protocol (including fresh DI water). Perform a prime protocol without loading your arrays. Failure to run a prime protocol will result in irreparable damage to the loaded hybridized arrays. Since the system is already well purged with water, you need not run an additional shutdown protocol. Just remove the old DI water bottle and replace it with a fresh bottle. Remove the DI water and perform a dry protocol shutdown. This will remove most of the water from the system and prevent unwanted microbial growth in the supply lines. Also, remove the pump tubing from the peristaltic pump rollers. NOTE: After you have completed the bleach protocol, discard the vials. NOTE: At this point you can, in the Configuration area, set the Bleach Interval Warning Limit and Bleach Interval Alert Limit. Click Save to save your configuration.

171 Peristaltic Tubing Maintenance appendix A The Fluidics Station 450Dx 169 You must periodically replace the peristaltic tubing because of wear, contamination, or in order to avoid salt buildup. Inspect the tubing on a weekly basis, if you see evidence of these conditions, follow the procedure outlined below. If you have AMDS administrator privileges, you can set the Change Tubing Warning Limit and Change Tubing Alert Limit. See the section, Managing the Fluidics Station, on page 114. Wear gloves when changing tubing. Do not allow fluid from old tubing to spill onto surfaces. IMPORTANT: For systems in routine use, Affymetrix recommends monthly replacement of the silicone peristaltic tubing (part number ). To ensure proper performance, use only tubing available from Affymetrix. This tubing is manufactured to the required specifications to ensure proper fluid delivery and array performance. You can obtain additional tubing by ordering from Affymetrix: Setting the Peristaltic Tubing Maintenance Parameters You should set the peristaltic tubing maintenance parameters when you or the service engineer originally set up the fluidics station or after you have replaced the peristaltic tubing. 1. In the AMDS software, click the System Management button the menu (Figure A.20).

172 170 The AMDS User s Guide Rev. B Figure A.20 Click the System Management button to gain access to maintenance functions. 2. The System Management window appears. The User Performed Service window should be the default window. If not, select In-House Service User Service. The User Performed Service window appears. Note the fluidics station maintenance area (Figure A.17). Figure A.21 The user maintenance functions for the fluidics station 3. From the dropdown list, select a station number. The system will show the last bleach and peristaltic tube change. 4. Select the Change Tubing procedure from the dropdown list and click the Perform button. The Confirm Step dialog box opens. Enter your password and event reason. AMDS enters the time and date information into the device log.

173 Replacing the Peristaltic Tubing Procedure appendix A The Fluidics Station 450Dx Open the module door. See Figure A.1 on page 139 (component number 2) and Figure A.22. Peristaltic Tubing Figure A.22 Module door open showing peristaltic tubing 2. Open the white clamps to release tubing on both sides. See Figure A.23.

174 172 The AMDS User s Guide Rev. B WARNING: Do not remove the module. Do not attempt to replace the tubing on a module where the module has been removed from the case of the fluidics station. In this case, rotating the pump may damage the motor driver circuitry. White Clamp Figure A.23 Releasing the peristaltic tubing 3. Pull tubing off while gently turning the peristaltic pump head. Discard old tubing. 4. Replace tubing with new peristaltic tubing supplied with the accessory kit as described below: a. Attach one end of the new tubing to the fitting on the right at the top of the pump enclosure.

175 appendix A The Fluidics Station 450Dx 173 b. Insert the tubing into the clamp under the fitting without stretching the portion of the tubing between the fitting and the clamp. There should be a small amount of slack in that portion of the tubing. c. Work the tubing into the pump head while slowly turning the pump. d. Insert the free end of the tubing into the other clamp, and attach it to the other fitting. 5. Close the drop-down module door. 6. Order more replacement tubing (P/N ). NOTE: At this point you can, in the Configuration area, set the Change Tubing Warning Limit and Change Tubing Alert Limit. Click Save to save your configuration. Fluidics Station Troubleshooting and Assistance If problems arise with the fluidics station, use the following tables to locate the description that matches the problem. If you cannot find a solution, call Affymetrix Technical Support for assistance. Troubleshooting Decision Tree The following simple flow charts (Figure A.24 and Figure A.25) show you how to begin troubleshooting the FS450Dx for a Missing Fluid Error (MFE).

176 174 The AMDS User s Guide Rev. B Figure A.24 Troubleshooting decision tree, page 1

177 Figure A.25 Troubleshooting decision tree, page 2 appendix A The Fluidics Station 450Dx 175

178 176 The AMDS User s Guide Rev. B Problems and Solutions This section lists some alert messages, the possible causes and solutions (Table A.2). AMDS may display these as alerts. To resolve these alerts, follow the recommended resolution in the current Worklist window on the alert panel. Table A.2 Problems and Solutions Error Message Problem Possible Cause Possible Solution (Follow the recommended resolution in the current Worklist window on the alert panel.) Missing Fluid Error Cartridge not filling completely with sample solution or buffer during initial stages of hybridization wash or staining protocol. Possible holes in the septa of the cartridge. Sample or staining solution not in place properly. In the current Worklist window on the alert panel, follow the recommended resolution. In the current Worklist window on the alert panel, follow the recommended resolution. Make sure sample or stain vial is in the sample holder. In the current Worklist window on the alert panel, follow the recommended resolution. You may need to add more sample solution to the sample vial. Blocked sampling tube or line of the fluidics station. Failure of one of the fluidics sensors. Pump tubing stretched too tightly around the pump. Call Affymetrix technical support for service. In the current Worklist window on the alert panel, follow the recommended resolution. You may need to loosen the tubing clamps, allow tubing to relax, close the clamps.

179 appendix A The Fluidics Station 450Dx 177 Table A.2 Problems and Solutions (Continued) Error Message Problem Possible Cause Insufficient volume of sample or staining solution (500 µl). Blocked sampling tube or line of the fluidics station. Possible Solution (Follow the recommended resolution in the current Worklist window on the alert panel.) In the current Worklist window on the alert panel, follow the recommended resolution. You may need to run a Prime script with fresh deionized (DI) water to flush out salt blockage. Cartridge not filling completely with buffer during wash script Buffer bottle empty. Module not primed. Fill buffer bottles. Prime module. Missing Fluid Error (continued) System detects improper conditions while filling. Note where in protocol error occurred. Missing or insufficient stain or antibody in vial? Wash empty? Air bubbles in line? In the current Worklist window on the alert panel, follow the recommended resolution. Leaks? Recovered less sample than initial input during Recover script. Loose tubing attachments inside the fluidics station. Call Affymetrix technical support for service. Fluidics Station X Does Not Respond Power not switched on at the fluidics station. Incorrect fluidics station designated for communication. Loose cables. Turn fluidics station power on, and then try to connect again. Designate correct fluidics station on workstation. Firmly connect cables to fluidics station. Sensor Timeout Sensor Timeout error message on workstation. No user response to Remove Vial prompt or other prompt. In the current Worklist window on the alert panel, follow the recommended resolution.

180 178 The AMDS User s Guide Rev. B Table A.2 Problems and Solutions (Continued) Error Message Problem Possible Cause Possible Solution (Follow the recommended resolution in the current Worklist window on the alert panel.) Cartridge is not filling or draining properly. Defective septa in cartridge. In the current Worklist window on the alert panel, follow the recommended resolution. You may need to: Error While Draining Error While Filling Insufficient sample or stain volume. Excessive bubbling in cartridge. Buffer conductivity too low. Failure of one of the fluid sensors. Use a new cartridge. Add more sample solution to sample vial. Change the buffer: reduce detergent. Call Affymetrix technical support for service. Error While Filling System detects improper conditions while filling. Note where in protocol error occurred. Missing or insufficient stain or antibody in vial? Wash or DI water empty? Air bubbles in line? Identify if chip is filled: In the current Worklist window on the alert panel, follow the recommended resolution. Leaks? Invalid Command Communication error detected Note where in protocol error occurred. In the current Worklist window on the alert panel, follow the recommended resolution. You may need to: Identify if chip is filled. Contact Affymetrix for service.

181 appendix A The Fluidics Station 450Dx 179 Table A.2 Problems and Solutions (Continued) Error Message Problem Possible Cause Possible Solution (Follow the recommended resolution in the current Worklist window on the alert panel.) Temperature Timeout Temperature does not reach specified temperature. Temperature has not reached required level in expected time if ambient temperature is within operating specifications (15 to 30 degrees C). Call Affymetrix technical support for service. Improper Script Script does not work. User is attempting to run a FS400 or FS450 script on FS450Dx In the current Worklist window on the alert panel, follow the recommended resolution. You may need to download proper FS450Dx script and continue. Valve Motion Error In the current Worklist window on the alert panel, follow the recommended resolution. If problem persists, contact Affymetrix for service. Valve Not Homed In the current Worklist window on the alert panel, follow the recommended resolution. If problem persists, contact Affymetrix for service. Valve Out of Position In the current Worklist window on the alert panel, follow the recommended resolution. If problem persists, contact Affymetrix for service.

182 180 The AMDS User s Guide Rev. B Meaning of Error Messages The following lists some of the common error messages and what they mean (Table A.3). AMDS may display these as alerts. To resolve these alerts, follow the recommended resolution in the current Worklist window on the alert panel. Table A.3 Error Messages Error Message Invalid Command Improper Script Temperature Timeout Sensor Timeout Valve not Homed Valve Motion Error Valve out of Position Error while Filling Error while Draining Meaning (Follow the recommended resolution in the current Worklist window on the alert panel.) The script contains a command that can not be executed because its command code is either undefined or has a format error. The first command of the script is not the required FS450Dx command. The Re-attempt command timed out before the set point temperature was reached. The Await Sensors command timed out before the anticipated sensor pattern was seen. The Home command did not result in the valve reaching it HOME position. The Valve command did not result in the valve reaching it target valve position. According to the outer valve encoder, the valve did not reach a valid position when it was last rotated. While filling the cartridge, the AwaitMotor command terminated because of the step count not the expected sensor pattern, and that the same error had occurred several times consecutively. While draining the cartridge, the AwaitMotor command terminated because of the step count not the expected sensor pattern, and that the same error had occurred several times consecutively.

183 appendix A The Fluidics Station 450Dx 181 Table A.3 Error Messages (Continued) Error Message Meaning (Follow the recommended resolution in the current Worklist window on the alert panel.) Stage C WashA Sense/Threshold 960/890 The Pump command completed its step count before the conductivity sensor determined that the cartridge contained a solution with conductivity below the set threshold value. Missing Fluid Error Examples: Stage C WashA Sense/Threshold 960/890 The Missing Fluid Error (MFE) Display not only gives a visual notification of an error condition to the operator, but gives you information that enables you to determine the cause of the error. It does this by displaying information about the sensor value and the fluid that caused the error. It shows this internal information in a continuous loop until the machine is powered down or a script is started. For example: Missing Fluid Error for 4 seconds Stage A valvepos WashA for 4 seconds Sense/Threshold 820/600for 4 seconds

184 182 The AMDS User s Guide Rev. B Other Problems and Solutions Table A.4 lists uncommon problems and their solutions. AMDS may display these as alerts. To resolve these alerts, follow the recommended resolution in the current Worklist window on the alert panel. Table A.4 Other Problems and Solutions Problem Air bubbles left in cartridge at the end of a hybridizationwash script. Buffer leaking inside the fluidics station. Cartridge needles of the fluidics station not engaging with the cartridge. Possible Cause Air bubble in wash line Loose tubing attachments inside the fluidics station. Washblock requires replacement. Salt buildup in the lines of the fluidics station. Possible defective septa on the cartridge. Extra flashing on the cartridge. Salt buildup on the cartridge needles. Cartridge holder aligned and attached to the fluidics station improperly. Possible Solution (Follow the recommended resolution on the alerts panel.) You may need to perform a Cleanout procedure or a Priming procedure. Call Affymetrix technical support for service. Call Affymetrix technical support for service. Run the Prime script with fresh DI water to flush out salt blockage. Use another cartridge. Use another cartridge, or call Affymetrix technical support for service. Run the Prime script with fresh DI water to flush out salt blockage. Clean cartridge needles with a wet cotton swab. Call Affymetrix technical support for service. Cartridge holder not properly engaged to the fluidics station. Place the cartridge into the cartridge holder. Push the holder door shut, and firmly lift the lever to engage the cartridge needles.

185 appendix A The Fluidics Station 450Dx 183 Table A.4 Other Problems and Solutions (Continued) Problem Sample needles do not properly enter vial. Possible Cause Bent sample needle User may be pressing the needle lever down to quickly or with too much force. Possible Solution (Follow the recommended resolution on the alerts panel.) Replace sample needle. Engage sample needle lever more slowly and/or with less force.

186 184 The AMDS User s Guide Rev. B FS450Dx LCD Messages This section describes the LCD script messages and their meaning (Table A.5). The following is a list of some of the common messages that appear on the fluidics station LCD throughout the course of the fluidics station operation. The actual list of messages on a particular fluidics station may include some that are not listed here (Table A.5). Table A.5 LDC Messages Message Changing --> Draining to Waste Purging with A Draining to Vial 1 Draining to Vial 2 Draining to Vial 3 Filling with A or Filling with B EJECT WASHBLOCK LOAD CARTRIDGE REMOVE PREVIOUS VIALS Meaning Wait for temperature to reach set point Empties cartridge. Purges chip with ~ 1mL of buffer A at 25 C from bottom to top then to waste. Recovers stain to Vial #1 for reuse or disposal. Recovers stain to Vial #2 for reuse or disposal. Recovers stain to Vial #3 for reuse or disposal. Drains and fills cartridge with last wash solution used, if any. Disengage washblock. Prompt for loading cartridge. Prompt to remove vials. LOAD VIALS Prompt for loading vials 1, 2, and 3. LOAD VIALS 1& 2 Prompt for loading vials 1 and 2. LOAD VIALS 1& 3 Prompt for loading vials 1 and 3. LOAD VIAL 1 Prompt for loading vial 1. LOAD VIAL 2 Prompt for loading vial 2. LOAD VIAL 3 Prompt for loading vial 3. Filling with A Filling with B Draw 1st Stain Empty, fill with wash-a, mix by drain-and-fill, repeat, leave cell full. Empty, fill with wash-b, mix by drain-and-fill, repeat, leave cell full. Empty, draw sample to both sensors.

187 appendix A The Fluidics Station 450Dx 185 Table A.5 LDC Messages (Continued) Message Draw 2nd Stain Draw 3rd Stain EJECT CARTRIDGE ENGAGE WASHBLOCK DO CLEAN CYCLE REMOVE STAIN VIALS LOAD 3 EMPTY VIALS Purging with water Washing needle 1 Purging with air Washing needle 2 Washing needle 3 Washing Lines Meaning Empty, draw sample to both sensors. Empty, draw sample to both sensors. Prompt for removal of cartridge. Prompt for engagement of washblock. Begin cleaning cycle. Prompt to remove stain vials, if present. Prompt to load vials. Purge with 5mL water to clean line. Performing wash needle #1 procedure. Purge with air. Performing wash needle #2 procedure. Performing wash needle #3 procedure. Wash tube from valve to waste. Prime Lines Equilibrate tube from valve to waste with wash A. REMOVE ALL VIALS Prompt to remove vials. LOAD SAMPLE VIAL IN LOC 1 Prompt for loading sample vial in location 1. Flushing with WashA Flushing with wash solution A. Filling with WashA A washes D/F Empty, fill with wash-a, mix by drain-and-fill, repeat, leave cell full. Wash with A by mixing using drain-and-fill procedure. Flushing with Wash Flushing with wash solution B. B washes D/F REMOVE SAMPLE VIAL LOAD EMPTY VIAL IN LOC 1 Wash with B by mixing using the D/F (drain-andfill) procedure. Make sure sample vial is removed. Make sure empty vial is present. Flushing with Wash Flushing with wash solution B.

188 186 The AMDS User s Guide Rev. B Table A.5 LDC Messages (Continued) Message Draining to Waste Meaning Drain waste. needle 1 w/wash Flush needle 1 with Wash B. Washing needle REMOVE VIAL Washing done READY Wash needle with water. Prompt to remove vial. Completion of washing. System is ready.

189 appendix A The Fluidics Station 450Dx 187 The FS450Dx Instrument Specifications Fluidics Station Dimensions: (height, depth, width) 40.2 x 41.0 x 71.1 cm or 15 13/16 x 16 1/8 x 28 inches Product Weight: Approximately 80 pounds or 36.3 kg Power Input: 100 to 240 V~, 3 A 300 watts or less Main supply voltage fluctuations not to exceed 10% of the nominal supply voltage. Temperature: Operating: 15 to 30 C Storage (non-operating):-10 to 60 C Humidity: Other: Operating: 10-90% RH, non-condensing Storage (non-operating):10% to 95% RH Pollution degree, 2 Installation category, II Electrical Supply The electrical supply shall meet the input specified on the instrument label. Voltage fluctuations shall not exceed 10% nominal supply voltage. Altitude <2000m

190 188 The AMDS User s Guide Rev. B Regulatory Compliance CE Mark Declaration of Conformity We, Affymetrix, Inc. 890 Embarcadero Drive West Sacramento, CA declare under sole responsibility that the Affymetrix GeneChip 3000Dx v.2, including Scanner model GCS 3000Dx, the AutoloaderDx, Fluidics Station FS450Dx, and associated Workstation with Molecular Diagnostic System software, is Manufactured in the United States of America, with U.S. and Non-U.S. components, and conforms with the relevant provisions of the following standard(s) of safety and compliance, and/or other normative document(s): EU In-Vitro Diagnostic Medical Devices Directive 98/79/EC, Annex III CE Declaration: ISO 13485:2003 Medical devices -- Quality management systems -- Requirements for regulatory purposes EU EMC Directive 89/336/EEC: EN :1997+A2:2001 EN 55011:1998+A2:2002 EN :2000 EN :1995 +A1:2001 EN :1995 EN :1995 EN :1995 EN :1995 EN :1996 EN :1994 Equipment for Measurement Control and Laboratory Use Limits and methods of measurements of radio disturbance characteristics of industrial, scientific and medical (ISM) radio frequency equipment Limits for harmonic current emissions (equipment input < 16A per phase) Limitation of voltage fluctuations and flicker in low voltage supply systems for equipment with rated current < 16A Electrostatic discharge immunity Radiated, radio frequency, electromagnetic field immunity Electrical fast transient/burst immunity Surge immunity Immunity to conducted disturbances, induced by radio frequency fields Voltage dips, short interruptions and voltage variations immunity

191 appendix A The Fluidics Station 450Dx 189 EU Low Voltage Directive 73/23/EEC: EN :2002 EN :1994 +A2:2001 Safety requirements for electrical equipment for measurement, control and laboratory use, Particular requirements for in vitro diagnostic medical equipment Safety of laser products Part 1: Equipment classification, requirements and user's guide Regulatory This device complies with Part 15 of FCC Rules. Operation is subject to the following two conditions: (1) This device may not cause harmful interference, and (2) This device must accept any interference received, including interference that may cause undesired operation. This Class A digital apparatus meets all requirements of the Canadian Interference-Causing Equipment Regulation. Cet appareil numérique de la classe A respecte toutes les exigences du Règlement sur le matériel broullier du Canada. Regulatory Agency Certification Compliant with directive 2002/96/EC (WEEE)

192 190 The AMDS User s Guide Rev. B China RoHS Restriction of Hazardous Substances Compliance Manufacturers of Electronic Information products (EIPs) that are sold to the People's Republic of China, are required to provide information about lead, cadmium, mercury, hexavalent chromium, polybrominated biphenyls and polybrominated diphenyl ethers contained within. In accordance with the Chinese RoHS (Restriction of Hazardous Substances), Table A.6 contains information identifying the specific hazardous material(s) and the components/parts in which they are found. Table A.6 Table Containing Names and Contents of Toxic or Hazardous Materials a Instrument: Affymetrix GeneChip Fluidics Station 450Dx Component /Part Categories Lead (Pb) Mercury (Hg) Cadmium (Cd) Hexavalent Chromium (Cr 6) Polybrominated Biphenyls (PBBs) Polybrominated Diphenyl Ethers (PBDEs) Printed Circuit Boards X O X O O O Rubber & Plastic Parts O O O O O O Electrical Components X O O O O O Internal Metal Parts O O O O O O External Metal Parts O O O O O O Labels O O O O O O Packaging/ Shipping Materials Internal Lasers, Optics & Sensors O O O O O O O O O O O O Adhesives O O O O O O

193 appendix A The Fluidics Station 450Dx 191 Table A.6 Table Containing Names and Contents of Toxic or Hazardous Materials a Instrument: Affymetrix GeneChip Fluidics Station 450Dx Component /Part Categories Lead (Pb) Mercury (Hg) Cadmium (Cd) Hexavalent Chromium (Cr 6) Polybrominated Biphenyls (PBBs) Polybrominated Diphenyl Ethers (PBDEs) Internal Power Supplies X O X O O O Motors and Pumps O O O O O O a X = Indicates that the toxic or hazardous substance contained is above the limit of 1000 ppm for lead and above 100 ppm for cadmium O = Indicates that the toxic or hazardous substance contained is below the limit of 1000 ppm for lead, mercury, hexavalent chromium, polybrominated biphenyls and polybrominated diphenyl ethers; and below 100 ppm for cadmium.

194 192 The AMDS User s Guide Rev. B SJ/T 电子信息产品污染控制标识要求 目前许多电子信息产品由于功能 性能或生产技术的需要, 仍含有大量如铅 (Pb) 汞 (Hg) 镉 (Cd) 六价铬 [Cr (Ⅵ)] 多溴联苯 (PBB) 和多溴二苯醚 (PBDE) 等有毒有害物质或元素 这些含有毒有害物质或元素的电子信息产品在废弃之后, 如处置不当, 不仅会对环境造成污染, 也会造成资源的浪费 因此, 为了达到节约资源 保护环境的目的, 以有毒有害物质或元素的减量化 替代为主要任务的电子信息产品污染控制工作已经提到政府主管部门的议事日程 为此, 信息产业部等七部委以 从源头抓起, 立法先行 的思路和原则, 制定了 电子信息产品污染控制管理办法 ( 信息产业部 39 号部长令, 简称 管理办法 ), 以立法的形式, 推动电子信息产品污染控制工作, 旨在从电子信息产品的研发 设计 生产 销售 进口等环节限制或禁止使用上述六种有毒有害物质或元素 为了进一步落实 管理办法 并达到限制有毒有害物质或元素在电子信息产品中使用的目标, 必须有配套使用的统一的标识方法标准 因此, 为了配合中华人民共和国 管理办法 的实施, 同时也为中华人民共和国信息产业界对六种有毒有害物质或元素铅 (Pb) 汞 (Hg) 镉 (Cd) 六价铬 [Cr (Ⅵ)] 多溴联苯 (PBB) 和多溴二苯醚 (PBDE) 的测试提供一个统一的标识方法, 特制定本标准 ( 表 Table A.7). a Table A.7 有毒有害物质或元素名称及含量 仪器 : Affymetrix GeneChip Fluidics Station 450Dx 部件名称 铅 (Pb) 汞 (Hg) 镉 (Cd) 六价铬 [Cr (Ⅵ)] 多溴联苯 (PBB) 多溴二苯醚 (PBDE) 印制电路板 X O X O O O 橡胶和塑料元件 O O O O O O 电子元件 O O O O O O 内部金属零件 外部金属零件 X O O O O O O O O O O O 标签 O O O O O O 组装 / 装货资料 O O O O O O

195 appendix A The Fluidics Station 450Dx 193 Table A.7 有毒有害物质或元素名称及含量 a 仪器 : Affymetrix GeneChip Fluidics Station 450Dx (Continued) 部件名称 内部激光, 光学器件和传感器 铅 (Pb) 汞 (Hg) 镉 (Cd) 六价铬 [Cr (Ⅵ)] 多溴联苯 (PBB) 多溴二苯醚 (PBDE) O O O O O O 胶粘剂 O O O O O O 内部电源 X O X O O O 马达和唧筒 O O O O O O a : 表示该有毒有害物质至少在该部件的某一均质材料中的含量超出 1000 ppm 铅 (Pb) 100 ppm 镉 (Cd) 的标准规定的限量要求 : 表示该有毒有害物质在该部件所有均质材料中的含量均在 1000 ppm 铅 (Pb) 汞 (Hg), 六价铬 [Cr (Ⅵ)], 多溴联苯 (PBB), 多溴二苯醚 (PBDE), 100 ppm 镉 (Cd) 的标准规定的限量要求以下 电子信息产品污染控制标识要求 (Marking for Control of Pollution Caused by Electronic Information Products) SJ/T

196 194 The AMDS User s Guide Rev. B This page left intentionally blank.

197 Appendix B THE SCANNER 3000DX WITH AUTOLOADERDX Introduction This chapter describes how to use the GeneChip Scanner 3000Dx with AutoLoaderDx (aka the AutoLoaderDx). The AutoLoaderDx is used as part of the overall assay workflow. Affymetrix has designed the AutoLoaderDx expressly for scanning multiple array cartridges. The AutoLoaderDx can scan up to 48 arrays automatically without operator presence. Figure B.1 The Affymetrix AutoLoaderDx

198 196 The AMDS User s Guide Rev. B WARNING: Do not remove the external case or skin or scanner cover of the AutoLoaderDx. Use the AutoLoaderDx only as instructed in this user guide. Do not attempt to service the instrument. Only qualified service technicians can open and service the AutoLoaderDx. There are no customer serviceable parts. Removing the case exposes the customer to laser and electrical shock hazards. Safe Operation To ensure safe operation of the AutoLoaderDx: IMPORTANT: Shutting down the AutoLoaderDx: To preserve the lifetime of the scanner's internal laser we recommend that you turn the scanner OFF when it is not in use for any extended period of time, such as overnight or a weekend. Read this section completely before operating the instrument. Do not attempt to service this instrument. Any attempt at unauthorized service may damage the instrument and/or void the warranty. The instrument weight is approximately 63 pounds (28.6 Kg). Do not place it on an unstable cart, stand, or table. Failure to properly support the instrument may cause serious damage or injury and may void the warranty. CAUTION: Heavy object. Two people are required to lift the AutoLoaderDx. The instrument must be surrounded by adequate airspace. Slots and openings in the instrument and the electronics compartment covers are for ventilation. Do not block or cover them.

199 appendix B The Scanner 3000Dx with AutoLoaderDx 197 Never push an object into the instrument ventilation slots; equipment damage or injury may result. Do not set liquids on top of the instrument. The instrument has an AC receptacle with a safety ground appropriate for the country of destination. The plug is designed to connect only to a 3-prong ground receptacle. This safety feature should not be compromised in any way. If the instrument AC plug does not mate with the available power source receptacle, consult a licensed electrician to install one that does. When to Contact Affymetrix Under any of the following conditions, unplug the instrument from the power source and contact technical Support: When the power cord is damaged or frayed. If any liquid has been spilled into the instrument. If the instrument has been penetrated by water. If, after service or calibration, the instrument does not perform in accordance with the capabilities stated in the specifications. If the instrument has been dropped or otherwise damaged. If the instrument must be returned for repair, call Affymetrix technical support. Laser Safety The laser is equipped with an automatic shutter that inhibits its output beam and ensures safe operation under conditions encountered in normal operation. The instrument covers, the array access port, and protective shutters ensure that during instrument operation no directed or stray laser light leaves the instrument. IMPORTANT: The AutoLoaderDx is a Class I laser product when the laser is enclosed in scanner case. The laser itself is a Class IIIB laser product.

200 198 The AMDS User s Guide Rev. B DANGER Laser radiation when open. Avoid direct exposure to laser beam. The lasers can cause serious injury if the instrument is not operated in accordance with instructions in this user guide. CAUTION Use laser safety glasses when servicing DO NOT STARE INTO LASER BEAM. The green laser is a 532nm solid-state laser. This is a Class IIIb laser and has visible outputs greater than 5mw but not more than 500mw. It must never be operated in an exposed manner. Any object in the direct path of the laser beam may be damaged. Eyes and skin can be seriously damaged by direct exposure to, specular reflections from, or diffuse reflections from this laser. If improperly used, a laser of this type can cause fires. When used according to the instructions in this manual and when all covers are in place, the GeneChip AutoLoaderDx is classified as a Class I Laser Device per 21 CFR Always take note of laser safety labels; they indicate areas where exposure to laser beams may be hazardous.

201 appendix B The Scanner 3000Dx with AutoLoaderDx 199 Electrical Safety The scanner will automatically handle any input voltage from 100 to 240 VAC nominal, 50 to 60 Hz NOTE: The scanner s power supply will autodetect the input voltage source and configure itself. CAUTION The power supply cord is used as the main disconnect device. Ensure that the socket outlet is located and installed near the equipment and is easily accessible. CAUTION: If you use the AutoLoaderDx in a manner not specified in this user guide, you may impair the protection provided by the equipment. CAUTION: Do not confuse your company s network connections with the dedicated Ethernet port of the AutoLoaderDx-workstation. The proper AutoLoaderDx connection is located near the top of the workstation. CAUTION: This 10/100 Base T Ethernet communications port is dedicated to the AutoLoaderDx-workstation interface. You cannot connect the AutoLoaderDx to your company s Ethernet communications network.

202 200 The AMDS User s Guide Rev. B IMPORTANT: The reset button is the scanner s circuit breaker. The breaker switch will be tripped whenever the scanner experiences an electrical fault condition. Press to reset. If you cannot reset this switch, contact Affymetrix technical support. Workstation - AutoLoader Connections Figure B.2 and Figure B.3 show the cable connections of the workstation and the AutoLoader. This is for reference only. Affymetrix recommends that only a qualified service technician attempt to service or change these connections.

203 appendix B The Scanner 3000Dx with AutoLoaderDx Pronged Electric Power Plug Fluidics Station 450Dx Connection AutoLoaderDx Ethernet Connection Firewall Connection Figure B.2 Workstation rear cable connections

204 202 The AMDS User s Guide Rev. B Circuit Breaker Reset Button Cable Receptacle to Workstation Power Cable Upper Drain Tube Lower Drain Tube Figure B.3 AutoLoaderDx rear connections

205 appendix B The Scanner 3000Dx with AutoLoaderDx 203 Connecting the Barcode Reader 1. Connect the barcode reader carriage to the workstation s USB port (Figure B.4). 2. Connect the barcode reader carriage to the USB cable and power cable (Figure B.4). Barcode Reader USB Port Barcode Reader USB Connection Power Connection Figure B.4 Workstation and barcode reader connections

206 204 The AMDS User s Guide Rev. B AutoLoaderDx Indicator Lights and On/Off Button The front panel has the following button and indicators (Figure B.5). 1. Purple AutoLoaderDx Indicator Light 2. Purple Scanner Indicator Light 3. Green light 4. I/O (on/off) button 5. Yellow light Figure B.5 The AutoLoaderDx indicator lights 1. Purple indicator light on AutoLoaderDx, running vertical at front center. This light appears to be merely an extension of the lower scanner light. However, when on, it indicates that the AutoLoaderDx door is closed and locked. It will turn off when the door is unlocked.

207 appendix B The Scanner 3000Dx with AutoLoaderDx Purple scanner indicator light on the AutoLoaderDx body, running vertical at front center. This light extends to the bottom of the AutoLoaderDx and is always on when the scanner is on. 3. Green light a. On = System is ready to scan (yellow off) b. Flashing = Scan in progress 4. I/O (on/off) button in the center. 5. Yellow light a. On = Idle, laser is warming up (laser not ready, green off) b. Off = System ready, no errors (Green on) c. Flashing = Error Summary of Indicator Lights The table (Table B.1) below summarizes the light conditions and their meaning. Table B.1 Light colors and meanings Condition Green Light Yellow Light Purple Scanner Indicator Light Purple AutoLoaderDx Indicator Light Meaning Initial boot up Scanner boot up Off Off On Off Initial power up; embedded PC takes control On On On Off Embedded PC takes control of scanner boot up

208 206 The AMDS User s Guide Rev. B Table B.1 Light colors and meanings (Continued) Condition Green Light Yellow Light Purple Scanner Indicator Light Purple AutoLoaderDx Indicator Light Meaning Laser warm up System ready Off On On Off Software enabled and laser is warming up On Off On Off Scanner ready for use and AutoLoader Dx door is unlocked waiting to receive a carousel Error Off Flashing On Off Fatal error, reboot scanner and software, AutoLoader Dx door is unlocked to remove carousel if necessary Scanning Flashing Off On On Scanning is in progress and AutoLoader Dx door locked Scanning Flashing Off On Off Scanning is in progress and AutoLoader Dx door is unlocked

209 appendix B The Scanner 3000Dx with AutoLoaderDx 207 Scanning Arrays This section shows you how to scan multiple arrays using the AutoLoaderDx. The GeneChip arrays are similar to those shown in Figure B.6. Figure B.6 The array, or cartridge: note the location of the flange. The AutoLoaderDx will accept the array in only one orientation. Using Tough-Spots to Prevent Leaks Tough-Spots are chemically inert polyvinyl labels that adhere to all plastics. Affymetrix recommends using 3/8-inch circle diameter Tough-Spots to prevent leakage from the array cartridge septa. Before loading the array cartridge into the AutoLoaderDx, follow this procedure to prevent the leaking of fluids from the array during scanning. Even if you have already applied Tough-Spots to the array prior to hybridization or after washing, you must remove the old Tough-Spots and apply new ones before you load them into the AutoLoaderDx. Affymetrix recommends the use of Tough-Spots obtained from Affymetrix P/N or from USA Scientific, Inc. P.O. Box 3565 Ocala, FL (800)LAB-TIPS P/N On the back of the array cartridge, clean excess fluid from around septa (Figure B.7).

210 208 The AMDS User s Guide Rev. B 2. Carefully apply one Tough-Spot over each of the two septa. Press to ensure that the spots remain flat. If a Tough-Spot does not apply smoothly; that is, if you observe bumps, bubbles, tears or curled edges, do not attempt to smooth them out. Remove the spot and apply a new one (Figure B.7). Tough-Spots TM Figure B.7 Applying Tough-Spots to array cartridge septa Loading Arrays into the Carousel 1. Load your arrays into the carousel (up to 48). Note that only one orientation is possible (Figure B.8). Arrays should be loaded into the carousel starting at position #1. Additional arrays need not be contiguous. The AutoLoaderDx will always scan and check all 48 slots starting a position #1.

211 appendix B The Scanner 3000Dx with AutoLoaderDx 209 Figure B.8 Loading the arrays into the chip carousel, note that each slot is numbered 1 through 48, and each array can fit in only one orientation.

212 210 The AMDS User s Guide Rev. B Loading the Carousel into the AutoLoaderDx 1. If you have previously removed the carousel from the AutoLoaderDx. Load the carousel into the AutoLoaderDx by inserting the carousel into the AutoLoaderDx and turning the carousel until the alignment pin seats into the alignment hole (Figure B.9). Alignment Hole Carousel Mounting Key Flat Alignment Key in the Autoloader Alignment Pin Inserting Carousel into the AutoLoaderDx Figure B.9 Loading the carousel into the AutoLoaderDx

213 appendix B The Scanner 3000Dx with AutoLoaderDx Turn the carousel clockwise until the carousel mounting key flat seats gently into the AutoLoaderDx alignment key. You may have to turn the carousel several times before it will seat into the alignment pin and alignment key. When seated properly, the carousel will be flush with the AutoLoaderDx housing. Close the AutoLoaderDx door (Figure B.10). Figure B.10 Inserting and turning the carousel; the carousel should be seated and flush with housing. NOTE: The seating of the key flat is confirmed by a gentle falling of the carousel into the key.

214 212 The AMDS User s Guide Rev. B NOTE: AUTOROTATION Starting the AutoLoaderDx The AutoLoaderDx has a heater to warm up the arrays prior to scanning in order to reduce condensation and fogging of the array window. The AutoLoader uses a process called autorotation to maintain the temperature stability of the carousel. The AutoLoaderDx spins the carousel around during the autorotation routine. This occurs only after the AutoLoaderDx run is complete or during a power failure as described below. Autorotation occurs during a power failure only if the uninterrupted power supply (UPS) is included as an accessory. The UPS provides power to the AutoLoaderDx during a power failure. If the power fails during the scan of an array, that scan is completed and then the system turns off the heater and enters the autorotation mode to conserve power and cool the chips in the carousel. During a scanning run, the carousel rotates to introduce the next array into the AutoLoaderDx, so autorotation is not needed. After the scanning run is complete, the AutoLoaderDx turns off the heater and rotates the carousel to get even cooling of the arrays. 1. Press the I/O button on the front panel to turn on the instrument. 2. Wait ten minutes for the AutoLoaderDx to warm up. Shutting Down the AutoLoaderDx 1. Press the I/O button on the front panel to turn off the instrument.

215 appendix B The Scanner 3000Dx with AutoLoaderDx 213 IMPORTANT: Affymetrix recommends a professional service call for maintenance at least twice a year. Please contact Affymetrix technical support for details. Cleaning and Maintenance The AutoLoaderDx requires little in the way of customer maintenance. The instrument must be kept clean and free of dust. Dust buildup can degrade performance. Wipe the exterior surfaces clean using a mild dish detergent solution in water. Do not use ammonia based cleaners or organic solvents, such as alcohol or acetone, to clean the system because they may d213mamage the exterior surfaces. Clean the carousel by hand using warm water and, if necessary, mild detergent. The Affymetrix Genechip Microarray Instrumentation System for IVD use requires calibration and maintenance twice a year by authorized Affymetrix personal to ensure the system performance. Failure to maintain the system as recommended may result in the failure of the system to perform in accordance with specifications published by Affymetrix. Configuring the AutoLoaderDx If you are an administrator, you can control three functions of the scanner (Figure B.11). You can: Turn on and warm up laser when you launch AMDS. Run the scanner one specimen at a time in manual mode. Disable the AutoLoaderDx to run only the software. Figure B.11 The user maintenance functions for the AutoLoaderDx

216 214 The AMDS User s Guide Rev. B Turn on Laser at Startup 1. Click on the System Management button. 2. Select Turn on Laser at Startup box (Figure B.11). Enable Manual Mode 1. Click on the System Management button. 2. Select Enable Manual Mode box (Figure B.11). Disable AutoLoaderDx 1. Click on the System Management button. 2. Select Disable AutoLoader box (Figure B.11). Troubleshooting This section deals with issues and problems that might occur with the AutoLoaderDx. Troubleshooting the AutoLoaderDx This section deals with issues relating primarily to the scanner part of the AutoLoaderDx especially when the AutoLoaderDx is in Manual Mode. Table B.2 AutoLoaderDx Troubleshooting Problem Possible Cause Corrective Action No image when scanning Intermittent problems scanning Power off or cable loose Loss of laser power Loose cable Check all connections and power. Contact technical support. Check all rear connections.

217 appendix B The Scanner 3000Dx with AutoLoaderDx 215 Table B.2 AutoLoaderDx Troubleshooting Problem Possible Cause Corrective Action AutoLoaderDx fails with array inside Power failure Manually extract array. Check all connections to AutoLoaderDx. Turn AutoLoaderDx on, restart software. Issues Relating to the AutoLoaderDx s Operation In using the AutoLoaderDx you may encounter some issues, or problems, that may require your intervention. Below is a list of these issues. Table B.3 Issues that may affect the AutoLoaderDx Issue If communications are interrupted during a scan (by a faulty cable connection or power being lost at the scanner, for example) Explanation AMDS will properly note the failure and present an alert that says Cannot connect to Scanner or something similar. However, there are two issues to note. first, AMDS will report such a failure only after a network time-out of about 30 seconds. Second, rarely, if communications have been lost, AMDS and the AutoLoaderDx may not be able to automatically restore communications once the problem is rectified, and both may become unresponsive. To restore proper operation, verify that the AutoLoaderDx is on, that communication cables are properly connected. See the section, Changing the Instrument Settings, on page 113. Click the Restart Scanner button to restart the AutoLoaderDx. You may need to close AMDS and restart Windows then restart AMDS. If the system remains unresponsive, disconnect and reconnect power to the scanner, restart the scanner normally, close and restart Windows and AMDS.

218 216 The AMDS User s Guide Rev. B Table B.3 Issues that may affect the AutoLoaderDx (Continued) Issue Repeated attempts to send commands (Start, Turn Laser On, etc.) from AMDS to the Scanner while AMDS is reporting the scanner Offline may result in AMDS becoming unresponsive until communications are restored If the Scanner experiences multiple autofocus failures, the system may enter an unresponsive state. Laser warm-up lasts for ten minutes, during which time the Turn Laser On button will remain unchanged and AMDS will display the status message Warm-up. If no array is inserted and a scan started. Autofocus will fail if salt deposits accumulate on the array. Explanation If communications cannot be re-established, follow the recommendations of item 1. Follow the recommendations of item 1 to restore communications and correct operation. Simply note that this is normal operation. The scanner will attempt go through the first parts of the auto-focus routine and then report Failed to find chrome border. Use Tough-Spots to prevent leaks in the GeneChip array. See the quick reference card, p/n , or the section, Using Tough-Spots to Prevent Leaks on page 207.

219 appendix B The Scanner 3000Dx with AutoLoaderDx 217 Troubleshooting the AutoLoaderDx This section deals primarily with diagnosing problems that may occur to the AutoLoaderDx. Table B.4 AutoLoaderDx Troubleshooting Guide Problem Possible Cause Corrective Action Intermittent problems scanning Scanner fails with array inside Carousel does not automatically home Carousel does not rotate Carousel misses next array Loose cable Power failure Check for stuck array Carousel not seated on D ring Alignment Pin not engaged in Carousel Door is open or ajar Door is open when purple LED is off. Door is open or ajar System is warming up, array in heater Carousel not seated on D ring Alignment Pin not engaged in Carousel Laser in Scanner is warming up. AMDS has Start grayed out in this case Array UP sensor not working, call technical support. Check all rear connections. Manually extract array. Check all connections to scanner. Turn scanner on, restart software. Stuck array See the section, Manually Removing a Lodged Array Cartridge, on page 220

220 218 The AMDS User s Guide Rev. B Table B.4 AutoLoaderDx Troubleshooting Guide (Continued) Problem Possible Cause Corrective Action AutoLoaderDx freezes up AutoLoaderDx overheats Autofocus routine fails to conclude Door is open or ajar Heater Failure TE failure TE hot fans vent blocked Salt buildup on array cartridge substrate Call technical support. Call technical support. Check for salt on chrome border. Use Tough-Spots to prevent leaks in the GeneChip array. See the quick reference card, p/n , or Using Tough-Spots to Prevent Leaks, on page 207. The array does not descend into scanner. Carousel not seated correctly Door is open or ajar Heater is waiting until array is at temperature. AutoLoaderDx Error Messages The following error messages indicate a serious malfunction of the AutoLoaderDx. Your arrays, or the data generated from them, may be at risk. You should shut down the AutoLoaderDx and remove the carousel. Do not continue to use the AutoLoaderDx in Automode. Call Affymetrix Technical Support. Table B.5 AutoLoaderDx Error Messages HEATER_LOW Message Meaning Warning: The warming chamber temperature is low. Refer to the troubleshooting guide.

221 appendix B The Scanner 3000Dx with AutoLoaderDx 219 Table B.5 AutoLoaderDx Error Messages (Continued) Message COLD_CHAMBER_LOW COOL_HOTSIDE_HIGH COLD_CHAMBER_HIGH HEATER_HIGH Meaning Warning: The cold chamber temperature is low. Refer to the troubleshooting guide. Warning: The cooler hot-side temperature is high. Refer to the troubleshooting guide. Note: Before calling technical support, check around the ventilation vents to ensure that nothing is blocking them. Warning: The cold chamber temperature is high. Refer to the troubleshooting guide. Note: Before calling technical support, check the AutoLoaderDx door to ensure that it is not open. Warning: The warming chamber temperature is high. Refer to the troubleshooting guide.

222 220 The AMDS User s Guide Rev. B Manually Removing a Lodged Array Cartridge In the event that a array becomes lodged in the array transport mechanism, follow the procedure outlined below. 1. Turn the AutoLoaderDx off and remove the power cord from the back of the unit. 2. Open the AutoLoaderDx door on top of the unit. 3. Remove the carousel from the system. (Keep the arrays in carousel and at the proper temperature while recovering the array still in the AutoLoaderDx). 4. Remove the hole plug, which is just in front of the array slot in the base piece of insulation. In the photo to the right, the screwdriver is inserted into this hole. 5. Using a standard, flat (-) screwdriver, ( ) gently slide it down through the hole making sure not to damage the shaft and spring that are protruding into the hole. When the screwdriver stops, it should be in contact with the scanner Y stage screw. Slowly turn the screwdriver until you feel it engaging the slot on the screw of the scanner Y stage.

223 appendix B The Scanner 3000Dx with AutoLoaderDx Slowly turn the screw clockwise until it hits a hard stop and cannot turn further. (Do not try to turn it further or use excessive force because it will break the Y stage in the AutoLoaderDx). The Y stage has now ascended to its maximum position. 7. Using your fingers, slowly slide the slot pin, which is sticking through the slot in the base piece of insulation, to the right until it stops. You should see the little pinch rollers near the array slot close a little as you do this. Pinch Rollers Slot Pin

224 222 The AMDS User s Guide Rev. B 8. Insert a 3/16 hex driver (Affymetrix P/N ) into the hole that is located on the front of the AutoLoaderDx housing on the left. You should feel it engage a coupling. 9. Turn the hex driver counter clock wise until you see the array appear through its opening. (The array should stay up if you stop turning the hex driver). If you don't see the array after turning the hex driver ten seconds go to step Grab and hold the array with your fingers. Using your other hand slowly slide the slot pin (Step 7) back to the left. This should open up the pinch rollers. Pull the array out.

225 appendix B The Scanner 3000Dx with AutoLoaderDx If you do not see the array after turning the hex driver for 10 seconds, stop. 12.Using tool (Affymetrix P/N ) with the hook down and toward the back, slide it vertically down against the front of the array opening, about 1.5 inches. (There is a small groove made for this tool in the middle of the front array guide) 13.Pull the top finger grip of the tool toward the front of the unit, and then pull it up while still putting pressure towards the front. The array should come up with the tool. When you see it, grab the array and pull it out of the unit. 14.If you cannot get the array out after doing this procedure, call for Affymetrix technical support. 15.Put the hole plug back into the hole in the base piece of insulation. 16.Plug the AutoLoaderDx back in and turn it on. 17.Load the carousel after the AutoLoaderDx boots up. 18.If arrays continue to become lodged in the AutoLoaderDx, you should call technical support.

226 224 The AMDS User s Guide Rev. B The AutoLoaderDx Specifications Table B.6 The Specifications of the Scanner 3000Dx with AutoLoaderDx Item Parameter Value Weight Shipping approx 115 pounds (52.2 Kg) Free-standing approx 100 pounds (45.4 Kg) Dimensions Width ~13.25 in. Power Depth Height Voltage Current Line Frequency. ~21.25 in. ~32 in V ~ 4-2 A Hz Working Environment Temperature 59 F-85 F (15 C-30 C) Humidity Clearance 10-90% Noncondensing 2 in. (5 cm) on side, back 12.5 in. on top Pollution Degree 2 Installation Category II Altitude <2000m Electrical Supply Main Supply Voltage Fluctuations Provide voltage, frequency or power rating per unit label Are not to exceed ±10% of the nominal supply voltage

227 appendix B The Scanner 3000Dx with AutoLoaderDx 225 Regulatory Compliance CE Mark Declaration of Conformity We, Affymetrix, Inc. 890 Embarcadero Drive West Sacramento, CA declare under sole responsibility that the Affymetrix GeneChip 3000Dx v.2 Instrumentation, including the Scanner GCS 3000Dx, the AutoloaderDx, the Fluidics Station FS450Dx, and associated Workstation with Molecular Diagnostic Systems software, is Manufactured in the United States of America, with U.S. and Non-U.S. components, and conforms with the relevant provisions of the following standard(s) of safety and compliance, and/or other normative documents: EU In-Vitro Diagnostic Medical Devices Directive 98/79/EC, Annex III CE Declaration: ISO 13485:2003 Medical devices -- Quality management systems -- Requirements for regulatory purposes EU EMC Directive 89/336/EEC: EN :1997+A2:2001 EN 55011:1998+A2:2002 EN :2000 EN :1995 +A1:2001 EN :1995 Equipment for Measurement Control and Laboratory Use Limits and methods of measurements of radio disturbance characteristics of industrial, scientific and medical (ISM) radio frequency equipment Limits for harmonic current emissions (equipment input < 16A per phase) Limitation of voltage fluctuations and flicker in low voltage supply systems for equipment with rated current < 16A Electrostatic discharge immunity

228 226 The AMDS User s Guide Rev. B EN :1995 EN :1995 EN :1995 EN :1996 EN :1994 Radiated, radio frequency, electromagnetic field immunity Electrical fast transient/burst immunity Surge immunity Immunity to conducted disturbances, induced by radio frequency fields Voltage dips, short interruptions and voltage variations immunity EU Low Voltage Directive 73/23/EEC: EN :2002 EN :1994 +A2:2001 Safety requirements for electrical equipment for measurement, control and laboratory use, Particular requirements for in vitro diagnostic medical equipment Safety of laser products -- Part 1: Equipment classification, requirements and user's guide

229 appendix B The Scanner 3000Dx with AutoLoaderDx 227 Regulatory This device complies with Part 15 of FCC Rules (Table B.7). Operation is subject to the following two conditions: (1) This device may not cause harmful interference, and (2) This device must accept any interference received, including interference that may cause undesired operation. This device complies with FDA performance standards for laser products except for deviations pursuant to Laser Notice No. 50, dated July 26, This Class A digital apparatus meets all requirements of the Canadian Interference-Causing Equipment Regulation. Cet appareil numérique de la classe A respecte toutes les exigences du Règlement sur le matériel broullier du Canada. Table B.7 Regulatory Certifications Regulatory Agency Certification Class I Laser Device Complies with EN : A2:2001. Complies with FDA performance standards for laser products except for deviations pursuant to Laser Notice No. 50, dated July 26, 2001 Hand held barcode reader is a Class II laser device Complies with EN : A2:2001. Complies with FDA performance standards for laser products except for deviations pursuant to Laser Notice No. 50, dated July 26, 2001 Compliant with directive 2002/96/EC (WEEE)